[gmx-users] Local pressure profiles

Philip Shushkov philip.shushkov at gmail.com
Thu Jun 5 18:42:44 CEST 2008

In fact I tried this first, but the message was quite disappointing:

Fatal error: 3921wat.5ns.oneside.pot.all.trr.trj does not exist.

I could not make the program to read in the file in trr format because it
always required the trj format. I am sorry but I have no experience with the
old versions of GROMACS. May be it is a stupid mistake but I could not
resolve the issue.


2008/6/5 David van der Spoel <spoel at xray.bmc.uu.se>:

> Philip Shushkov wrote:
>> Dear Prof. van der Spoel,
>> I have made new *.tpb file with the old grompp version after some changes
>> of the simulation parameters such as switching to cut-off electrostatics and
>> replacing lincs with shake, but now I think that I have problem with the
>> trajectory file. I converted the trr file into trj file as is required by
>> the program using the trjconv program. My pbc seem to be normal in the
>> trajectory file because the simulation was carried out in NVT ensemble but
>> when starting the mdrun patched with local pressure code I received the
>> following message:
>> trn version: GMX_trn_file
>> Reading frame       0 time    0.000   Warning: Only triclinic boxes with
>> the first vector parallel to the x-axis and the second vector in the
>> xy-plane are supported.
>>         Box (3x3):
>>            Box[    0]={5.35555e-315,  0.00000e+00, 5.35555e-315}
>>            Box[    1]={ 0.00000e+00, 5.43969e-315,  0.00000e+00}
>>            Box[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>         Can not fix pbc.
>> And in the log file the pbc that were read from tpb file are:
>> box (3x3):
>>   box[    0]={ 4.88021e+00,  0.00000e+00,  0.00000e+00}
>>   box[    1]={ 0.00000e+00,  4.88021e+00,  0.00000e+00}
>>   box[    2]={ 0.00000e+00,  0.00000e+00,  2.00000e+01}
>> I hope that there is a solution of the obstacle again.
>> Thank you very much in advance for your help.
>> Best regards,
>> Philip
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Have you tried with the trr file? I don't see why it should not work.
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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