Hi Stephan, It all a matter of time scale. Large molecules ==> slower movements (compare trucks and motor-bikes).
Cheers, Itamar. On 1 February 2011 03:18, lloyd riggs <lloyd.ri...@gmx.ch> 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. > > 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 > -- -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================
-- 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
