Quoting Di Pan <[EMAIL PROTECTED]>: > Hi, All > > I do my md simulation for 30ns, but after 20ns the protein move out of > the box, so it seems that the protein is broken in .trr file. I try to > use trjconv to put the protein back into the box and make the protein > whole. The command is like below:
Read here: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions If the protein is just "diffusing out" of the box, there is no problem. If however, the protein "breaks," then there's likely a problem with your topology, but you are likely just seeing an effect of PBC. -Justin > trjconv trjc -f *.trr -o out.trr -s *.tpr -pbc nojump -center rect > > But after run the trjcov command, some parts of the protein is till out > of box, and seems like broken. > Is there anyone meed the same problem can tell me how to resolve this > problem. > > Thank you very much > > Di,Pan > > Di,Pan > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.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
