To wrap this up for anyone who stumbles across this in the future:
The 'solution' I ended up going with was to avoid using hydrogen atoms in
the restraints, instead restraining to the e.g. methyl carbon and adding a
fudge factor to the restraint length to account for the C-H distance.
This results
Have you tried with even less restraints? I found systems are not always
stable with more than the bare minimum of restraints
On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas wrote:
> It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
> an impact. I've tried being gentle,
It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
an impact. I've tried being gentle, slowly turning up the force constant
and running for 1 ns for each value but as soon as the force constant
approaches 100 it crashes.
The starting structure was generated with the same re
On Fri, Aug 30, 2013 at 8:56 AM, Trayder wrote:
> Hello,
> I am attempting to simulate a protein-ligand complex using distance
> restraints to match it to NMR data.
> The system runs stably without restraints. With restraints it tends to spit
> out LINCS angle warnings and blow up under most condi
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