Hi Morteza, I had this problem when I was running a trimeric protein attached to an oligosaccharide.
*I have used the following command:* * * *trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol* * * *but it is not working.* Do the following. It worked for me. In the first round, run trjconv -f *.xtc -s *.tpr -center -boxcenter tric -pbc mol -o 1.xtc and choose backbone (which is usually 4 from the index) for centring. In the second round, use 1.xtc obtained from the first step and run the command as follows trjconv -f 1.xtc -s *.tpr -center -boxcenter tric -pbc a -o 2.xtc and this time also choose the backbone for centring. This should bring back the dimeric protein system in the box. Sometimes the water molecules around the edge are broken. Hope this is not a big worry. By the way is your box cubic or truncated octahedron? My case was a cubic box. Hope this helps. Regards Sai On Tue, Jun 8, 2010 at 2:23 AM, shahab shariati <[email protected]>wrote: > Morteza Khabiri wrote: > > > > Dear users > > > > I have a dimer protein in the water box. It was run for 30ns. > > during the simulation dimer split to two monomer. This things happen bc of > > PBC. ( I checked it by vmd pbc option ) > > to have a two monomer together during trajectories (for visualization) > > I have used the following command: > > > > trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol > > > > but it is not working. > > Is there any other method or command which I could implement pbc in > > trajectory. > > > > Thanks in advance > > > > Morteza > > > > > > > > Shahab Shariati wrote: > > > > You can use other flags of trjconv command as follows: > > > > Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center > > > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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