[gmx-users] Position restraint problem

Marcelo Silva jokler79 at hotmail.com
Tue Jan 18 00:01:19 CET 2011

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, continuing the equilibration at 298 K 
brings problems with PME (becomes very slow due to the cutoff). 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 

Thank you

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