[gmx-users] position restraints crashing

[Alan Dodd]

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...

----------------------------------------------------


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