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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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