Just to add to David's comment, did you take a look at the trajectory? What
are you restraining exactly? Could it be that the restraint for any reason
is crossing the PBC? I see you are wrapping the trajectory, and this could
be the source of the issue.
El sáb., 5 ene. 2019 a las 15:44, David Case (<david.case.rutgers.edu>)
escribió:
> On Fri, Jan 04, 2019, Kung, Ryan wrote:
> >
> >I am having trouble running restrained MD simulation with pmemd.cuda on
> >
> >and my restraint file is:
> >
> > &rst iat=-1,-1, r1=18.6, r2=28.6, r3=28.6, r4=38.6, rk2=10., rk3=10.,
> >ir6=0, ialtd=0, iresid=0, igr1=6229,6251,6252,6231,6294,6296,
> >igr2=9515,9516,9519, /
> > /
>
> Just to be sure: have you installed all updates, especially update.7,
> which addresses problems in using COM restraints in pmemd.cuda? Go
> to $AMBERHOME, and type "./update_amber --help" for information, and
> "./update_amber --update" to get your code up to date. Then, re-run
> configure and make.
>
> ....dac
>
>
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sat Jan 05 2019 - 07:00:02 PST
