[gmx-users] position restraints crashing

[Steffen Wolf]

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...
>
> ----------------------------------------------------
>
>
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-- 
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: swolf at bph.rub.de
Web: http://www.bph.rub.de