[gmx-users] running a simulation without production

Zuzana Benkova upolzben at savba.sk
Tue Nov 4 15:10:38 CET 2008

Dear Mark, 
Thank you very much for valuable advice. 
Previously, I run some simulations and I obtained what I had expected. For
instance, instead of the plate I have just used one single chain which was
treated as frozen and the simulations were running. I obtained all output
files containing appropriate information. 
I have GMX version 3.3.3. I have just tried gmxtest.pl test first in sthe
ingle precision. The output I got was

All 16 simple tests PASSED
FAILED. Check files in dec+water
FAILED. Check files in fe_test
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED

I am not very familiar with programming language C++. As I wanted to test
also the double precision I did some changes in the gmxtest.pl file. I am
not sure if I did it correctly. I have installed GMX with _mpi suffix, so I
have changed the sub setup_vars section 

sub setup_vars {
    my $mdprefix = "";
    if ( $parallel > 0 ) {
        $mdprefix = "mpirun -c $parallel ";

    if ( $double > 0 ) {
        $grompp = "grompp_mpi";
        $mdrun  = $mdprefix . "mdrun_mpi";
        $ref    = "reference_d";

and after applying command gmxtest.pl -double all I have obtained 

sh: line 1: 30240 Segmentation fault      mdrun_mpi >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
All 14 complex tests PASSED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED

In the case of the single precision test I can not figure out the error
since I do not have any new files produced after the test in corresponding
directories. In the case of double precision test I have also log file in
rb1 directory which has been terminated exactly in the same way as my
attempts to run simulation of plate-chain system. 

Please, could you give me some explanation and hints how to proceed further?
It would be very helpful for me. I have checked the mailing list but did not
find something that could help me. Thank you in advance.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: Monday, November 03, 2008 9:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] running a simulation without production

Zuzana Benkova wrote:
> I have tried also running this job without user specified potential, 
> with relaxed plate, with pbc=no and some other attempts, but I always 
> failed in the same way. I would be very thankful for suggestions how to 
> cope with this problem.

Do other simulations run? Try one of the tutorials or gmxtest.pl.

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