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