Why not use distance pulling? Then the pull_vec is defined by the vector separating the two pull groups.
Best, Erik 6 jul 2012 kl. 08.21 skrev Raj: > Hi all, > > I am working on steered molecular dynamics and In that I would like to pull > the ligand ( already in complex with protein) away from the reference amino > acid ( which I've selected so that I can direct the ligand to get closure to > my desired amino acid residue). Now the thing is when I used VMD to assign > the direction, The desired direction of mine is not along the proper x, y, > or in Z axis. So my question is how can i specify the direction in a > situation like this. I've seen in other discussions people have used > pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks > in advance > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists