[gmx-users] Local pressure profiles

[Philip Shushkov]

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


2008/5/30 David van der Spoel <spoel at xray.bmc.uu.se>:

> Philip Shushkov wrote:
>
>> Dear gmx-users,
>>
>> I would like to calculate the local pressure profile of lipid bilayer and
>> that's why I downloaded and installed the gromacs-localp package that was
>> contributed to the gromacs software by Lindahl and Edholm. The problem is
>> that I have already generated the trajectory of the bilayer and I would like
>> to rerun the simulation in order to recalculate the pressure profile.
>> However, the package I have downloaded is an old version of the gromacs
>> software and when I tried to read in the Version 3.3.3 tpb generated with
>> tpbconv from the original  *.tpr file I received the following error:
>>
>> Fatal error: reading tpx file (5ns.oneside.pot.restart.tpb) version 40
>> with version 20 program.
>>
>> I would like to ask whether there is a way to get around the problem and
>> has someone else encountered such a problem.
>>
>>  just make a tpr with the old gromacs.
>
>  Best regards,
>> Philip
>>
>>
>> ------------------------------------------------------------------------
>>
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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