[gmx-users] position restraints crashing

[Alan Dodd]

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 <swolf at bph.rub.de> 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 at 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
> gmx-users-request at gromacs.org.
> > 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: swolf at bph.rub.de
> Web: http://www.bph.rub.de 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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
> gmx-users-request at gromacs.org.
> 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