Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Dear Erik, Thank you. My gmx is 3.3.1. Maybe that's the reason there is no difference except documentation part. To my understanding to your email, gmx 3.3.1 has solved that problem. I don't know why I still encounter it. In fact, there is no COUL term in my coarse-grained FF. I don't know what i

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, I'm certainly seeing lots of differences between 1.5 and 1.5.4.1 when I run diff in my cvs tree. However, I think we made the 3.3.1 release after march 9, in which case it is included there. Cheers, Erik On Aug 5, 2006, at 12:05 AM, Dongsheng Zhang wrote: Dear Erik, I had the sam

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Dear Art, Thank you for sharing your tips. In my case, there is no COUL term in my coarse-grained force field. I just can't understand why the program stops without finding any error (It can continue by tpbconv). All the best! Dongsheng On Sat, 2006-08-05 at 11:16 -0700, Arthur Roberts wrote:

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, all, I was able to fix the problem by: 1) Reducing my PME order from 6 to 4 2) Reducing my Fourier spacing from 0.12 to 0.06 3) Also, I had to do comm_grps = System or comm_grps = Protein Best wishes, Art --- Dongsheng Zhang <[EMAIL PROTECTED]> wrote: > Dear Erik, > > I had the same probl

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follow

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi Art, you run a small system (4800 atoms) on a lot of CPUs (64). In the md.log file it says that you have 2 grid points per CPU for the parallel FFT (local_nx). There is indeed one limitation to the PME code in 3.3.1: you need at least 0.5*pme_order grid points per CPU. Your pme_order is 6. So

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, It _might_ be solved by the fix attachment at http://bugzilla.gromacs.org/show_bug.cgi?id=55 (also in CVS) Cheers, Erik On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote: Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. E

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Arthur Roberts wrote: Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub

[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hang

[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hang