Re: [gmx-users] Exact continuation run

From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Exact continuation run Date: Sun, 16 Sep 2007 12:33:52 +1000 (EST) Hi I have been running exact

[gmx-users] LINCS error

hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is

Re: [gmx-users] LINCS error

This is an issue that has been discussed a lot on the list. The typical reasons for LINCS errors can be found here: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Quoting vijay kumar hinge vijay [EMAIL PROTECTED]: hello users, i am using gromacs 3.3 version on unix platform i got

[gmx-users] TFE query

Hello gmx users, I have a query and would be greatfull if I could get some suggestions on the subject. I constructed a tfe.itp file with the parameters mentioned by Fioroni et. al., J. Phys. Chem. B 2000, 104, 12347-12354. I then generated a tfe.gro file

[gmx-users] ffgmx_lipids.tar.gz

Hi, I want to perform simulation of membrane protein . I try to downloaded the ffgmx_lipids from : http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar.gz But, corresponding webpage shows error, URL was not found. Plz attatch this files to my e-mail . I have

Re: [gmx-users] New single thread performance numbers

Florian Haberl wrote: Hi, Barcelona is out now and SPEC CPU2006 (www.spec.org) has released new numbers (I have taken them from the german c't magazin www.heise.de): Single core performance: 435.gromacs Opteron 235074.4 Opteron 51.1 Xeon X5365 143.3 Caveat that these

Re: [gmx-users] TFE query

Dilraj Lama wrote: Hello gmx users, I have a query and would be greatfull if I could get some suggestions on the subject. I constructed a tfe.itp file with the parameters mentioned by Fioroni et. al., J. Phys. Chem. B 2000, 104, 12347-12354. I then

[gmx-users] New single thread performance numbers

Hi, Barcelona is out now and SPEC CPU2006 (www.spec.org) has released new numbers (I have taken them from the german c't magazin www.heise.de): Single core performance: 435.gromacs Opteron 235074.4 Opteron 51.1 Xeon X5365 143.3 444.namd Opteron 235074.1 Opteron

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

parichita parichita wrote: Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please

Re: [gmx-users] interaction energy between the ligand and protein

Rui Li wrote: Hello! Can I estimate the inhibit capability by interaction energy between the ligand and protein? Only about as well as you can estimate the results of a Formula One racing season from the marks the drivers got on their drivers license exams. And how can I get the

Re: [gmx-users] New single thread performance numbers

thanks Andrew Stelzer University of Michigan Department of Chemistry and Biophysics 930 N University Ave Ann Arbor, MI 48109 On Sep 17, 2007, at 8:58 AM, Mark Abraham wrote: Florian Haberl wrote: Hi, Barcelona is out now and SPEC CPU2006 (www.spec.org) has released new numbers (I have

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background

Re: [gmx-users] ffgmx_lipids.tar.gz

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies should have roughly what you want. Failing that, google is your friend. - Original Message From: Rina Ghosh [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Monday, September 17, 2007 1:12:05 PM Subject: [gmx-users]

RE: [gmx-users] Exact continuation run

Hi I would need exact cintinuation runs for covariance analysis? From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Exact continuation run Date: Mon, 17 Sep 2007 10:10:28 +0200From: Mark Abraham Reply-To: Discussion list for

Re: [gmx-users] New single thread performance numbers

Hi, Yes, the SPEC numbers aren't representative for typical gromacs performance. Technically I'm still on NDA for the benchmarks I ran on Barcelona so I can't share the exact numbers with you, but on average the performance will be pretty much the same _per_clock_ as Intel Clovertown.

RE: [gmx-users] Exact continuation run

From: vijaya subramanian [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: RE: [gmx-users] Exact continuation run Date: Mon, 17 Sep 2007 14:17:01 + Hi I would need exact cintinuation

[gmx-users] Neutralising charge distribution

Hello I would like to ask what is the functional form of the uniform neutralising charge distribution applied in Gromacs when doing PME on a charged system. Is there a correction term for this charge distribution that is included in the calculation of energies? Thanks George

Re: [gmx-users] New single thread performance numbers

Hi Erik. Still under NDA? Haven't it been lift last sunday? Anyway: I don't know exactly the terms of the NDA, So if you can't answer me the following question, please say no, I can't answer. I'm in touch with people having some compability issues with their Barcellonas and MBs, so could you

[gmx-users] cgnr problems

Hi, In manual gmx 3.3, I find if possible, the total charge of a charge group should be zero . In my systems, I want to do an artificial charge distribution model. So I have some questions: 1. I don't know whether it is right that I don't make the total charge to zero in one charge

[gmx-users] g_rmsf and the -fit option , calculating average structures

I see to calculate the average structure of a protein in a trajectory minus any rotational + translational effects, using g_rmsf. Does the -fit option (default yes) eliminate rot + trans contributions? Or must one use trjconv first, to convert the trajectory to some reference frame

Re: [gmx-users] New single thread performance numbers

Hi Jones, On Sep 17, 2007, at 6:25 PM, Jones de Andrade wrote: Still under NDA? Haven't it been lift last sunday? Well, I guess it's because this was pre-release hardware, so it didn't have any expiry date :-) Anyway: I don't know exactly the terms of the NDA, So if you can't answer me

Re: [gmx-users] cgnr problems

wangcl wrote: Hi, In manual gmx 3.3, I find “if possible, the total charge of a charge group should be zero” . In my systems, I want to do an artificial charge distribution model. So I have some questions: 1. I don’t know whether it is right that I don’t make the total charge to

Re: [gmx-users] g_rmsf and the -fit option , calculating average structures

Arneh Babakhani wrote: I see to calculate the average structure of a protein in a trajectory minus any rotational + translational effects, using g_rmsf. Does the -fit option (default yes) eliminate rot + trans contributions? Yes, it will. If it can't rotate and translate, it's not much of a