[gmx-users] position restraints crashing

[Alan Dodd]

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
> 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?
> >
> >   
> 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
> 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 
> 
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