So let me see if I understand, should I use the same refc file for all
runs?
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.
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.
Thanks to everybody!
Fabian
On Oct 27, 2015 7:23 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Tue, Oct 27, 2015 at 1:04 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I think jason made a good point, but I expect that allowing the refc to
> > change for each run is more likely what's going on here. check that first
> > before doing NVT.
> >
>
> Ah, I read the OP has using the exact same restraint file. If that's not
> the case (but you are *updating* the restraint file each time), then this
> will certainly cause the effect you're seeing.
>
> That's also more consistent with the observations (i.e., that the total
> energy drops, which would happen if the restraint energy dropped to 0 if
> you always set -ref and -c to the same files).
>
> I agree with Carlos -- updating refc will *definitely* be a more noticeable
> effect than the restraint coordinate scaling.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Oct 27 2015 - 12:00:03 PDT
