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
