In fact I tried this first, but the message was quite disappointing:<br><br>Fatal error: 3921wat.5ns.oneside.pot.all.trr.trj does not exist.<br><br>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.<br>
<br>Philip<br><br><br><br><div class="gmail_quote">2008/6/5 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Philip Shushkov wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
Dear Prof. van der Spoel,<br>
<br>
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:<br>
<br>
trn version: GMX_trn_file<br>
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.<br>
Box (3x3):<br>
Box[ 0]={5.35555e-315, 0.00000e+00, 5.35555e-315}<br>
Box[ 1]={ 0.00000e+00, 5.43969e-315, 0.00000e+00}<br>
Box[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
Can not fix pbc.<br>
<br>
And in the log file the pbc that were read from tpb file are:<br>
<br>
box (3x3):<br>
box[ 0]={ 4.88021e+00, 0.00000e+00, 0.00000e+00}<br>
box[ 1]={ 0.00000e+00, 4.88021e+00, 0.00000e+00}<br>
box[ 2]={ 0.00000e+00, 0.00000e+00, 2.00000e+01}<br>
<br>
I hope that there is a solution of the obstacle again.<br>
Thank you very much in advance for your help.<br>
<br>
Best regards,<br>
Philip<br></div><div class="Ih2E3d">
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</div></blockquote>
Have you tried with the trr file? I don't see why it should not work.<br><font color="#888888">
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.</font><div><div></div><div class="Wj3C7c"><br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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