washington. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. The read speed of the trajectory will go much faster if you select the "load all at once" checkbox in the moleculeRe: Vibrational mode analysis. edu> wrote: > I'm cc'ing here the NAMD list so that others. RE: Force field design. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass""wrapAll on" with a complex. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message:. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. uiuc. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. Re: Protein in/out of box. double. washington. I made those videos seven years ago. 1002/prot. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. upenn. washington. edu> wrote: >> Hi! >> >> Are there any benchmarks available which compare the performance of NAMD on >> Lincoln (CUDA heterogenous cluster) with its performance on a traditionalVMD-L Mailing List. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. washington. Fwd: Installing NAMD on windows. edu> > wrote: > Roy, > > I think that you are confusing two things. washington. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. uiuc. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. washington. From: Gianluca Interlandi (gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. NAMD supports CHARMM22 parameter files. washington. Justin Kollman Professor. From: Gianluca Interlandi (gianluca_at_u. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorGianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by. washington. prm". washington. 7 ns/day, which seems decent given the system size. There have been over 180 downloadsGianluca Interlandi, Wendy Thomas, The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations, "Proteins: Structure, Function, and Bioinformatics",. Thanks for the reply. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. washington. <br> <br>1999 March: Degree in modern languages result 107/110 - University of Catania, Italy with a degree thesis on Irish. Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. Cancellation policy. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). Neil King Assistant Professor. Entertainment. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallIn reply to: Gianluca Interlandi: "Compiling NAMD 2. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. I am > using the option "wrapAll on". edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. Don't take my word that this works. I am > using the option "wrapAll on". edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. From: Gianluca Interlandi (gianluca_at_u. Eric Klavins Professor. gianluca@u. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. washington. You simply load your trajectory > into VMD Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. washington. washington. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. It's > slightly faster but still not that much faster than running on 16 CPU cores. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. From: Gianluca Interlandi (gianluca_at_u. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. edu> Date: Friday, May 4, 2007 6:53 pm Subject: Re: namd-l: query about wrapped coordinates > This script needs the information about the box size. Be the first to write a review. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. txt". washington. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates"In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. washington. 478 KJ/mol = 0. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Re: Abe versus Lincoln. washington. From: Gianluca Interlandi (gianluca_at_u. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. washington. unam. In this way, you could get a feeling what NAMD can do before you > invest money. Re: Langevin process in NAMD tutorial"Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. washington. Michel Espinoza-Fonseca: "Re: Vibrational. washington. Search 214,979,228 papers from all fields of science. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" INVENTING THE FUTURE OF MEDICINE. washington. From: Gianluca Interlandi (gianluca_at_u. uiuc. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. Forest, Academic Editor. washington. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Mitchell Gleed (aliigleed16_at_gmail. washington. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Gianluca Interlandi [email protected] orcid. washington. edu>> > > I suspect that E3_19 might not be stable with this type of > implicit solvent model (it doesn't contain a term to take the > non-polar solvation energy into accout). edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. Hope the video helps, but now I'm embarrassed. > However, topology and parameters for water and ions are. SMD on center of mass. Kitchen. washington. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). I was getting 2. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. Choose File -> Save Coordinates. But, using the PBC my protein is continuous. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. Michel Espinoza-Fonseca: "Re: Vibrational. washington. FimH. edu> > wrote: > Roy, > > I think that you are confusing two things. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass"Re: Abe versus Lincoln. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. washington. Cancellation policy. Next in thread: Gianluca Interlandi: "Re: NAMD 2. washington. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. washington. uiuc. C; the more troublesome part is the lack of long-range electrostatic treatments. Thomas, 2 , * and Evgeni V. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. 7b1 on NCSA Abe. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. }, author={Dagmara I. washington. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the. This is unrelated to KDE3. From: Gianluca Interlandi (gianluca_at_u. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. I want to simulate a protein > attached to mannose. Re: Protein in/out of box. washington. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. VMD-L Mailing List. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. uiuc. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. > > Forget about creating a pdb file. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. Next in thread: Gianluca Interlandi: "Re: Should you cap C and N termini?" Reply: Gianluca Interlandi: "Re: Should you cap C and N termini?" Messages sorted by: [ attachment ] We generally use caps because our systems are individual domains within larger proteins. From: Gianluca Interlandi (gianluca_at_u. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. Pavel Aprikian, # 1 Gianluca Interlandi, # 2 Brian A. PMID: 37700555; DOI: 10. edu> wrote:From: Gianluca Interlandi (gianluca_at_u. 5923 Kcal/mol also we have 6. 1002/prot. washington. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. washington. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. >> >> i am attaching some graphs with performance numbers from. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Next in thread: Gianluca Interlandi: "Re: NAMD 2. Kid friendly. (did you see if any hunk failed?)Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu: "Re: high (or low) pressure readings" Next in thread: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Brian Bennion: "Re: fatal error"> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu > <mailto:gianluca_at_u. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. I know this can be just a detail, but it is quite tricky. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. Search for: Main Menu. From: Gianluca Interlandi [gianluca_at_u. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. washington. Re: Yet another NAMD speed concerns. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. Reply: Gianluca Interlandi: "Re: Cuda benchmarks namd2. Abstract. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. uiuc. , Thomas W. Chemistry. 7 out the door on Friday. Kisiela, # 1 , * Hovhannes Avagyan, # 1 Della Friend, 2 Aachal Jalan, 1 Shivani Gupta, 3 Gianluca Interlandi, 3 Yan Liu, 4 Veronika Tchesnokova, 1 Victoria. washington. washington. Author Profile. In the text > field you can enter your atom selection, e. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. washington. VMD-L Mailing List. 6 version, although I am not running the cluster at full load yet. edu]Reply All Saturday,. I needed to install the 'patch' program. 6 version, although I am not running the cluster at full load yet. Just a good MD toy ! Victor owner-namd-l_at_ks. uiuc. Gianluca Interlandi. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" Complex between VWF A1 and GpIbα and amino acid sequence of the A1 domain. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. But not now. 6 ns/day for a 100k atom system with roughly those same parameters (and. . I needed to install the 'patch' program. washington. washington. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. washington. 1002/prot. 478 KJ/mol = 0. washington. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. I needed to install the 'patch' program. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. edu) Date: Wed Dec 12 2012 - 14:49:46 CST Next message: JC Gumbart: "Re: NAMD and new FF CHARMM36" Previous message: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" In reply to: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" Next in thread: Jeffrey Potoff: "Re: NAMD and new FF CHARMM36" > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. washington. edu> wrote: > Hi Fatemeh, > > Thanks for replying. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. I > would be happy if somebody could point me out to some scripts which help me > perform that. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. I made those videos seven years ago. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. washington. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. >From: Gianluca Interlandi (gianluca_at_u. washington. washington. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. at 298. The only significant change since 2. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. What are you trying to accomplish? Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a js Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. washington. New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. washington. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. washington. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. INVENTING THE FUTURE OF MEDICINE. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. Next in thread: Gianluca Interlandi: "Re: NAMD 2. washington. edu> wrote: > Hi Fatemeh, > > Thanks for replying. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. From: Stern, Julie (jvstern_at_bnl. E-mail: [email protected],. > > I am trying to open VMD remotely. Balcony. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Re: namd ibverbs. That file contains information how to run >> NAMD (and also compile it. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. Response Time: Within a few hours. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. Gianluca Interlandi Research Assistant Professor. e. unizh. From: Axel Kohlmeyer (akohlmey_at_gmail. Chemistry. Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce the. Member since 2014. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. washington. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiHosted by Gianluca Interlandi Ask a question. July; 84 (7):990–1008. From: Buddhadev Maiti (bmaiti_at_gsu. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. 15 K 1 KT = 2. I empolyed PBC condition with wraping water and wraping all options on. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. washington. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. You should simulateCorresponding Author. C; the more troublesome part is the lack of long-range electrostatic treatments. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. In reply to: Gianluca Interlandi: "Compiling NAMD 2. g. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. edu> > wrote: > Roy, > > I think that you are confusing two things. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. Choose File -> Save Coordinates. J. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file.