If irest=0, no velocities should be used (even if ntx=5). I think you need
to use ntx=5 so sander/pmemd knows that velocities are present (if there is
periodic box information). If this is not the case, I think this probably
needs to be fixed...
All the best,
Jason
On Wed, Jul 4, 2012 at 11:33 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Hey,
>
> I am using sander from Amber 11 and read coordinates and velocities from
> an MD restart file via ntx=5. However, I want to generate new
> velocities, i.e. not use the velocities from the restart file. So I set
> irest=0, ig=-1, tempi=300. But it seems like the velocities from the
> restart file are not overridden by randomly generated ones. In this
> case, I had to use ntx=1 (which seems to also work with restart files
> and not only with plain coordinate files).
>
> Is it new in Amber 12 that irest=0 leads to velocities from an MD
> restart file being ignored? The Amber 12 manual says for this setting
> "Velocities in the input coordinate file, if any, will be ignored".
>
> Thanks,
>
> Jan-Philip Gehrcke
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 04 2012 - 09:30:03 PDT
