Hi Stephan, On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote:
> Dear All, > > A quick question as I have not really delved into code for gromacs ever, nor > know anyone close whom has worked on it. > > If I set up an MD simulation using a 4 protein complex, and 1 small peptide, > plus waters, etc...and run the whole thing the proteins never move, only the > amino acids within(constant temp RT and pressure 1 bar). > > Two domains make one complex, and another two the other. Basically, if I > seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift > (the chains) towards each other, but the two large (global) protein units > never move their center (I know I can make it work with Pull vectors, but why > not in the simple system with a generated initial randomized velocities), I > woundered why they are fixed in a normal run with minimal parameters? Is > there a reason (specific to developers), historical reason, or other? As > waters move around fine, and anything else added (salt, small molecules of > 20-30 atoms, water) except the central molecule(s) of interest. In a 'normal' run they should not be fixed. Could it be that you did accidentally fix them by specifying center of mass removal (comm-grps in .mdp)? Carsten > > Grüsse > > Stephan Watkins > -- > Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! > Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
