No, minimisation was without PR. Surely minimisation with PR would *increase* bad contacts, rather than removing them? I've tried running for a while under normal MD, successfully and without LINCS errors, then taking the endpoint and running under PR, but it still crashes almost instantaneously, so it's unlikely to just be a matter of energies or bad contacts, I'd have thought?
--- Steffen Wolf <[EMAIL PROTECTED]> wrote: > Hi Alan, > well, no, position restraints (and your definition) > seem to be fine, and > they work well with my protein/membrane system. > Sounds more like your > system is still not well minimized. Using the > freezegroup option is not > such a good way, because it will not work well > together with the > pressure coupling. Did you use the restraints during > minimization as well? > Bye > Steffen > > Alan Dodd wrote: > > Hello, > > I'm trying to run position restraints on multiple > > peptides in a protein/bilayer/water system. MD > > *without* position restraints runs absolutely > fine, > > but as soon as I stick that "define = -DPOSRES" > in, > > some of the molecules explode within a matter of > fs. > > Any idea why this might be? Is MD with position > > restraints considerably less tolerant of bad > > structures, energies etc (although the structure > > minimised absolutely fine-only "wrongness" about > it is > > a big hole)? > > Am using 3.2.1. Will probably try defining the > > protein as a freeze group as a temporary > get-around... > > but it'd be nice to find out what's going on. > > > > > > topol.top: > > ; > > ; File 'topol.top' was generated > > ; By user: ad0303 (1002) > > ; On host: hydra > > ; At date: Wed Aug 9 11:21:57 2006 > > ; > > ; This is your topology file > > ; ? > > ; > > ; Include forcefield parameters > > #include "ffgmx.itp" > > > > ; Include chain topologies > > #include "topol_A.itp" > > #ifdef POSRES > > #include "posre_A.itp" > > #endif > > > > #include "topol_B.itp" > > #ifdef POSRES > > #include "posre_B.itp" > > #endif > > > > #include "topol_C.itp" > > #ifdef POSRES > > #include "posre_C.itp" > > #endif > > > > #include "topol_D.itp" > > #ifdef POSRES > > #include "posre_D.itp" > > #endif > > > > #include "topol_E.itp" > > #ifdef POSRES > > #include "posre_E.itp" > > #endif > > > > #include "dopc.itp" > > > > ; Include water topology > > #include "spc.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 1 1 1000 1000 1000 > > #endif > > > > ; Include generic topology for ions > > #include "ions.itp" > > > > [ system ] > > ; Name > > ? > > > > [ molecules ] > > ; Compound #mols > > Protein_A 1 > > Protein_B 1 > > Protein_C 1 > > Protein_D 1 > > Protein_E 1 > > DOPC 256 > > SOL 9598 > > Cl 25 > > > > > ----------------------------------------------------- > > > > posre_whatever.itp (same for all 5 peptides) > > [ position_restraints ] > > ; atom type fx fy fz > > 1 1 1000 1000 1000 > > 5 1 1000 1000 1000 > > 6 1 1000 1000 1000 > > 7 1 1000 1000 1000 > > 8 1 1000 1000 1000 > > 10 1 1000 1000 1000 > > 11 1 1000 1000 1000 > > 12 1 1000 1000 1000 > > etc... > > > > > ---------------------------------------------------- > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > > > -- > Dipl.-Chem. Steffen Wolf > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: [EMAIL PROTECTED] > Web: http://www.bph.rub.de > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
