Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result? I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other. What does the output look like when you use the option -centre? If nothing else, seperating the commands might help you find the source of the problem.
----- Original Message ---- From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Tuesday, December 25, 2007 9:48:29 PM Subject: [gmx-users] image centering Dear users, I have a membrane simulation trajectory, in which the solvent (water and ions) is separated by lipid bilayer. I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell. I have tried the followings. trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole Both pbc and center didn't work. Is there any way to center the solvent? Happy holidays. -- 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
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