[gmx-users] Position restraint problem
Mark.Abraham at anu.edu.au
Tue Jan 18 00:16:40 CET 2011
On 18/01/2011 10:01 AM, Marcelo Silva wrote:
> Thank you Justin and Mark for your help. The problem is that I wasn't
> using the .gro file from the minimization step and it was giving a
> segmentation fault problem too, but I've corrected that problem, ran
> the simulated annealing without constraints and it worked fine.
> But I have another question. Since after this process the box becomes
> too large in NPT conditions,
In what sense?
> continuing the equilibration at 298 K brings problems with PME
> (becomes very slow due to the cutoff).
PME should be faster - the neighbour lists have fewer entries in them
and the cutoff should stay the same.
> Is it reasonable to take the last frame of the simulated annealing and
> pick one of the structures obtained as a starting structure for a new
I have no idea. Please leave the old context for the discussion when
posting a continuation. The only person with the incentive to remember
your whole context is you :-)
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