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
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 conditions.
I'm attempting to use:
; Restraints
disre
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