Dear All, I was setting up things to use COM pulling for a multiprotein complex. My question after going through the gromacs documentation(online) is:
Is there a way to limit either the time or distance two groups are pulled towards each other(reguarding only the applied force), as I could not find anything. Basically, if I run something in vacuo, the groups (proteins) do not move globally even when constraints, etc are set to none. To measure any Gibbs , delta H etc...I need the groups too move towards each other and form the interactions I am measuring, but do not want the pull force to interfear with overall calculations. My thoughts were to do a very short run, and then either remove the pull force, etc from the .mdp file, and use a checkpoint to re-start it, but do not know if this would work or would maintain the movement however arbitrary in the general correct direction. that or use such a small (.2 kcal/mol nm2) that it does not matter very much. Sincerely, Stephan Watkins -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
