[gmx-users] Position restraint problem

[Mark Abraham]

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 
> equilibration?

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 :-)

Mark