RE: [gmx-users] Scaling problems in 8-cores nodes with GROMACS 4.0x

Hi, This problem is not very strange at all. Different CPU's have different efficiencies for different types of code. In this case the Opteron and new Xeon have measurably different (although probably not more than 20%) relative performance for particle-particle and PME interactions. Also, your

Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

Hi Berk, Shorter tau_p? I thought you suggested 5.0 or 10.0 ps ? On Wed, Sep 2, 2009 at 5:28 PM, Berk Hess wrote: > Hi, > > I also just recalled that we have a bug report open since two years already > about drift of the COM: > http://bugzilla.gromacs.org/show_bug.cgi?id=165 > But in that case

RE: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

I meant 3 instead of 30 ps. I would say 1 ps is too short for systems with a phase with large molecules___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

[gmx-users] msd

Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decrea

[gmx-users] GROMACS in Windows Command Prompt

Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. I have just discovered that if I add the variable "GROMACS" with variable value "...path\GROMACS" in the System - Advanced - Environment Variables - User variables section of the control panel and also add t

Re: [gmx-users] GROMACS in Windows Command Prompt

George Tsigaridas wrote: Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. OK, so *use* the Cygwin shell... there are much easier ways of setting environment variables for the Cygwin shells than through the XP control panel (though, rarely, this can be n

RE: [gmx-users] msd

Hi, g_msd calculates the msd for molecules, not for atoms. I guess that would explain the result when you half the chain length. It might also explain the box size effects, since whole chains will still have a reduction in MSD due to periodiciy with a box of 3 Rg. If you run g_msd without -mol y

Re: [gmx-users] GROMACS in Windows Command Prompt

OK Mark. But at least, I wonder if the use of the command prompt is going to make easier the application of MPI in a PC network running Windows XP (see also my previous message). What's your opinion? Thanks George - Original Message - From: "Mark Abraham" To: "Discussion list for G

Re: [gmx-users] t_trxframe speed units

Hey, I tried everything you suggested and a couple more things and still it is not possible to get a reasonable speed for the pulled groups (always way beyond the 0.01nm/ps set in the mdp file and mostly containing some high frequence patttern probably related to pbc). (I tried: constraint, pbcato

RE: [gmx-users] t_trxframe speed units

Hi, The only thing I suggested was using pull_start=yes, otherwise you will start at a "random" distance and you will have enormous forces. Did you try that? Do you have a rectangular or a triclinic box? Berk > Date: Thu, 3 Sep 2009 18:00:44 +0200 > From: alexander.h...@mytum.de > To: gmx-us

Re: [gmx-users] mdrun running without simulating new steps

Hi Justin, I think it is the minimization issue. I did steep for 2000 steps, and it works thereafter for the mdrun, for this structure. Thank you very much! Regards, Stone Gao -- From: "Justin A. Lemkul" Sent: Tuesday, September 01, 2009 4:35 P

[gmx-users] g77 error in martini

Dear all, In the martini tutorial there is a approach of martini + ElneDYN . In the tutorial they provided me a script which converts the cleaned pdb structure to CG structure of protein. I compiled the script using g77 (as they recommended) and then I am trying to make the CG structure of 1BL8 pro

Re: [gmx-users] g77 error in martini

sunny mishra wrote: Dear all, In the martini tutorial there is a approach of martini + ElneDYN . In the tutorial they provided me a script which converts the cleaned pdb structure to CG structure of protein. I compiled the script using g77 (as they recommended) and then I am trying to make

[gmx-users] Problems with GROMAC/CPMD

Hello all. I have tried to perfomed some simulations about protein dynamics including one copper ion, close from the protein, by Gromacs/CPMD. However, I get some problems during CPMD simulation. In the *.mdp file I added the following: ---

[gmx-users] Problem with NPT equilibration

Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax < 1000 in 1785 steps Potential Energy = -1.6945709

[gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?

Hi The 3.3.3 and 4.0.5 version were installed under => * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* *The 4.0.5 version is currently the default one.* I want to compare the computation results from 4.0.5 version and 3.3.3 version. So, I write the *source /usr/gromacs/3

Re: [gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?

Chih-Ying Lin wrote: Hi The 3.3.3 and 4.0.5 version were installed under => * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* I've no idea what these scripts are, but the correct procedure is to follow the advice about GMXRC here: http://oldwiki.gromacs.org/index.php/In

Re: [gmx-users] Problem with NPT equilibration

Bing Bing wrote: Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax < 1000 in 1785 steps Potential E

[gmx-users] Bad water sampling ? => A charge group moved too far between two domain decomposition steps ???

Hi The system is "one lysozyme + water " running on 16 nodes. After => Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. --- Program mdrun_mpi, VERSION 4

Re: [gmx-users] Bad water sampling ? => A charge group moved too far between two domain decomposition steps ???

Chih-Ying Lin wrote: Hi The system is "one lysozyme + water " running on 16 nodes. After => Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. --- Progr

[gmx-users] Minimisation - particle decomposition

Hi No matter pbc = no or pbc = xyz Energy Minimisation is required with particle decomposition. That is, mdrun -pd is required. Why? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] The same lysozyme.pdb file under 3.3.3 and 4.0.5 version

Hi I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under 16 nodes. Simply, lysozyme.pdb + water. There is no problems (errors) with 3.3.3 version. However, with 4.0.5 version, the same lysozyme pdb file with the same simulation condition. except mdrun -pd with minimisation

Re: [gmx-users] The same lysozyme.pdb file under 3.3.3 and 4.0.5 version

Chih-Ying Lin wrote: Hi I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under 16 nodes. Simply, lysozyme.pdb + water. There is no problems (errors) with 3.3.3 version. However, with 4.0.5 version, the same lysozyme pdb file with the same simulation condition. except mdru