[gmx-users] position restraints crashing
anoddlad at yahoo.com
Thu Aug 10 13:37:10 CEST 2006
Interesting idea, but multiple different start points
have failed with PR, and succeeded with normal MD.
Freeze groups seem to be working OK, so I'm using that
for now - after all, it doesn't need to be 'real', I
just want to equilibrate the lipid/solvent without
moving my carefully-placed peptide.
Interestingly, I've had similar problems before, but
only when I use multiple peptides. Might try merging
the chains and see what that does.
I used CG with steep every 50 steps... sounds weird I
know, but it's proved pretty reliable.
--- Steffen Wolf <swolf at bph.rub.de> wrote:
> Alan Dodd wrote:
> > No, minimisation was without PR. Surely
> > with PR would *increase* bad contacts, rather than
> > removing them? I've tried running for a while
> > normal MD, successfully and without LINCS errors,
> > taking the endpoint and running under PR, but it
> > crashes almost instantaneously, so it's unlikely
> > just be a matter of energies or bad contacts, I'd
> > thought?
> Yes, so it looks that minimization ended at a
> metastable point, which
> was surmounted by a free MD run but kept by the PR
> and therefore caused
> the system to crash. Which minimization algorithm
> did you use? Steep or CG?
> Dipl.-Chem. Steffen Wolf
> Department of Biophysics
> University of Bochum
> ND 04/67
> 44780 Bochum
> Tel: +49 (0)234 32 28363
> Fax: +49 (0)234 32 14626
> E-Mail: swolf at bph.rub.de
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