I'd suggest this is an issue with VMD rather than gromacs. You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before. Normally, of course, PBC settings in Gromacs keep molecules whole in the output file quite reliably, but not knowing how you've set your simulation up, I couldn't comment on that. Using ngmx is a good way to check that Gromacs itself is doing what you think it is.
----- Original Message ---- From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Tuesday, January 15, 2008 2:51:20 PM Subject: [gmx-users] image control Dear users, I'm running NPT simulation POPC with a short peptide. I see the long bonds across the unit cell in VMD. Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? Some lipids move whole molecules, but some are broken. How can I control the unit of image? I couldn't find any related word in the manual. I assume image will be done by "residue". Then I shouldn't get this strange result. I got the popc.itp from Dr. Tieleman's web site. Any idea? -- Best wishes, MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -----Inline Attachment Follows----- _______________________________________________ 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 ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
_______________________________________________ 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
