On Tue, Oct 27, 2015 at 2:35 PM, Fabian Glaser <fabian.glaser.gmail.com>
wrote:
> So let me see if I understand, should I use the same refc file for all
> runs?
>
That depends. If you don't use the same one (but instead use the same as
the inpcrd file), you will always see a sharp reduction in the total
potential energy at the start of each simulation due to the drop in
potential energy.
I always use the same file for -c and -ref, but since I always discard the
restrained part of my simulation before analysis, it doesn't matter.
> In my example the original equil.rst?
>
> so the constraints will be always around the same position for every atom
> OK thanks! I think I understand my mistake.
>
The only "mistake" in using different restarts was the initial surprise at
the resulting energy jump across simulations. However, if you plan on
*using* the restrained trajectories during your analysis, you need to be a
lot more careful about exactly how you define those restraints (and I'd
recommend against doing that).
>
> I only use them since I have an array of peptides from the original unit
> cell that I want to keep more or less in place.
>
Well it's hard (impossible?) to say how those restraints are impacting the
thermodynamics of your simulation (or what effect it will have on the
MM-PBSA binding free energies you get from it). So it's something you
should think carefully about.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 27 2015 - 13:00:03 PDT
