Hi Pratul,
The maximum number of atoms in a COM group is capped at 200 atoms. It is a
hardcoded limit in pmemd (maxigr=1024).
It will also be helpful if you share your input files.
On Sun, Mar 10, 2019 at 3:11 PM Stephan Schott <schottve.hhu.de> wrote:
>
> Seems to be related to: http://archive.ambermd.org/201903/0056.html
>
> El dom., 10 mar. 2019 a las 19:51, Pratul Agarwal (<pratul.agarwal-lab.org
>)
> escribió:
>
> > Is there a limit for number of atoms that can be included in group(s)
> > while using COM restraints with pmemd.cuda v18?
> >
> > I am seeing significant divergence in restraint energy term between CPU
> > and GPU version, for groups with about 50 atoms. For smaller groups
with
> > ~20 atoms, GPU simulations appear to be stable and comparable to CPU
> > version. However, for groups with ~50 atoms the restraint energy term is
> > showing "*********" within ~2000 steps (= 4 ps), while CPU simulations
are
> > stable for same input.
> >
> > All patches have been applied including the relevant patch.7. Any
pointers
> > will be highly appreciated, and I am happy to provide more details.
> >
> > --
> > Pratul K. Agarwal, Ph.D.
> > (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> > Web: http://www.agarwal-lab.org/
> >
> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
> _______________________________________________
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--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 Email: kellon.belfon.stonybrook.edu
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Received on Sun Mar 10 2019 - 14:00:01 PDT
