Re: [gmx-users] Why does the -append option exist?

Hi Dimitar,Thanks for the bug report. Would you mind trying the test program I attached on the same file system that you get the truncated files on?compile it with gcc testje.c -o testioSander testje.c Description: Binary data On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:Hello,Just a quick

Re: [gmx-users] Reg:walls and pbc xy

The walls are simply interactions between the atomtype of the wall you specified (in your case opls_966 and opls_968), and the rest of the system, at the planes defined by z=0 or z=z_box. wall_type= 9-3 wall_r_linpot= 1 wall_atomtype = opls_966 opls_968 wall_density= 9-3 9-3

Re: [gmx-users] g_energy problem with 4.5.1 and 4.5.2

Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. Sander On 2 Nov 2010, at 10:28 , Michael Brunsteiner wrote: Hi everybody, I run NPT simulations (with the double precision version of mdrun) of a polymer melt with anisotropic pressure scaling The

Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

version). As Berk said, these issues are bad enough for a new version to be released soon. Sander On 2 Nov 2010, at 11:55 , Michael Brunsteiner wrote: Sander pronk wrote: Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. thanks for your swift reply! I

Re: [gmx-users] Center of Mass removal in a specified direction

One trick I am working with right now, is to have - periodic boundary conditions only xy - remove the COM motion of the water and the graphite separately. The COM motion is now removed only in the xy direction, so they are free to move in z. - put the surface (your graphite) at coordinate 0 -

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

, Carsten Kutzner wrote: Hi Sander, On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote: Hi Carsten, As Berk noted, we haven't had problems on 24-core machines, but quite frankly I haven't looked at thread migration. I did not have any problems on 32-core machines as well, only on 48-core

Re: [gmx-users] Gibbs free energy of binding

Hi Mohsen, The mean energy difference is only one component of the free energy difference. Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. There's a good reason free energy calculations cover

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi Carsten, As Berk noted, we haven't had problems on 24-core machines, but quite frankly I haven't looked at thread migration. Currently, the wait states actively yield to the scheduler, which is an opportunity for the scheduler to re-assign threads to different cores. I could set harder

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

:04 , Carsten Kutzner wrote: Hi Sander, On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote: Hi Carsten, As Berk noted, we haven't had problems on 24-core machines, but quite frankly I haven't looked at thread migration. I did not have any problems on 32-core machines as well, only on 48

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote: On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote: Thanks for the information; the OpenMPI recommendation is probably because OpenMPI goes to great lengths trying to avoid process migration. The numactl doesn't prevent migration as far

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: Recently I installed gromacs4.5.1 without mpi support on my workstation with 8 cores using cmake and make -j 8, make install commands ( as suggested on installation instructions). Now when I do mdrun it automatically utilizes all the

[gmx-users] Re: [gmx-developers] Free Energy Calculation

It sounds like there is something wrong with the 'B' topology. Have you tried the 'decoupling' .mdp parameters? They're there specifically for your type of calculations. Sander On Sep 2, 2010, at 04:58 , Emanuel Birru wrote: Hi, I am doing a partition coefficient of solute between

Re: [gmx-users] please, how edr data is xdr packed?

As David said, the reading/writing is done in src/gmxlib/enxio.c, but you could also read edr files indirectly through gmxdump: that should also give you an idea of the type of information in those files. On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote: Hi there, I am trying

Re: [gmx-users] tpi segmentation fault

Hi Javier, I've just committed a fix to the git 4.5 tree. Thanks for reporting this. Sander On 13 Aug 2010, at 18:35 , Javier Cerezo wrote: Hi all. I am trying to perform a tpi (test particle insertion) calculation on a trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a

Re: [gmx-users] error compiling gmx 4.5 on Mac 10.6.4

Hi Alan, I've fixed that bug yesterday; the fix should be in yesterday's new beta. Thanks for the bug report, Sander On 31 Jul 2010, at 12:41 , Alan wrote: Hi there, I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing: ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib

Re: [gmx-users] suitable parameter settings for intermolecular non-bonded interaction

Hi Vedat, If I understand it correctly, you're trying to calculate the free energy of binding using the LIE method. Then keep in mind that LIE is an approximate method, and that any accuracy you're trying to achieve is going to be limited by the approximations of LIE. Your 'primary

Re: [gmx-users] Signal 11 crash

Signal 11 on Linux is a segmentation fault: either you've hit a bug in mdrun, or there was some faulty input causing it to crash. You'll need to look at your md.log to see what happened. Sander On Mar 30, 2010, at 12:11 , 程迪 wrote: Hi, gmx-users I just encountered a singal 11 problem. I

Re: [gmx-users] git installation error

It looks like you're you're using gcc; is that right? If so, you're probably using an old (pre-2005) version. Try a newer one: it's free! Sander On Mar 30, 2010, at 13:00 , babu gokul wrote: I tried to install git version of Gromacs but when i make the file its shows the following error

Re: [gmx-users] gmx_fatal.c, line: 481

The reason grompp is failing is because there are some things it warns about (that's quite clear from your error message), and by default it will refuse to continue unless you explicitly tell it to. Without the actual warning there is very little we can do to help you. Sander On Mar 30,

Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

It sounds like the normal thing that would happen if you have a system that has no shear elastic constant, like a fluid. In that case, there are no restoring forces against growth of system size in one coordinate with a concomitant decrease in the other coordinates, so eventually this should

Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

setup with independent pressure coupling for each dimension (anisotropic)? Thanks, Sapna On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk pr...@cbr.su.se wrote: It sounds like the normal thing that would happen if you have a system that has no shear elastic constant, like a fluid

Re: [gmx-users] density tip3p

Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too

Re: [gmx-users] Free Energy Calculation

Hi Anirban, You *could* use the configurations in your trajectory to (re)calculate average energies; by de-coupling your ligand this would get you the average free energy change per coupling strength change at the point where the ligand is fully bound. If you're interested in free energy of

Re: [gmx-users] averaged pressure not consistent with set value

Pressure and volume are very slowly converging thermodynamic variables; it might very well be that your system hasn't converged yet. You should, however, see progression towards some average volume when you plot the volume as a function of time with g_energy. Sander On Mar 21, 2010, at

Re: [gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00

Those derivatives should be zero: the kinetic energy is determined by your thermostat and shouldn't change as a function of lambda - as it should for any normal free energy calculation in constant-temperature ensembles. Also, the constraint energy doesn't change as lambda changes (only the van

Re: [gmx-users] density

You got pretty close to what the density of SPC water is at 298K According to Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density, William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10, Pages 1179 - 1186

Re: [gmx-users] parallel mdrun

You need to run MPI jobs with 'mpirun'. The correct command would be mpirun -np 8 mdrun -s topol.tpr (I don't know what the -N 8 does). Sander On 16 Sep 2009, at 18:03 , Jarol E. Molina wrote: Hi all I have a single machine with multilpe processors. I want run mdrun with 8 processors

Re: [gmx-users] Core i7 vs Core2Quad

Hi, In Linux, one can apparently set processor affinity (or, in this case core affinity) with 'taskset'. The command is used like this: taskset bitmask command where bitmask is a hexadecimal bit mask with the cpus to use (in a format like 0xff, where 0xff enables the first 8 cpus on a