[gmx-users] Local pressure profiles

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 5 17:57:15 CEST 2008

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
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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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