Hi Giovanni,
Did you manage to experiment with this? I.e. what happens if you always make
-ref XXX = the inpcrd file.
Also can you try reducing your cutoff to 8 angstroms and see if the problem
still occurs?
All the best
Ross
> -----Original Message-----
> From: case [mailto:case.biomaps.rutgers.edu]
> Sent: Thursday, November 10, 2011 5:23 AM
> To: giovanni.pavan.supsi.ch; AMBER Mailing List
> Subject: Re: [AMBER] R: problem with pmemd.cuda
>
> On Thu, Nov 10, 2011, Giovanni Pavan wrote:
> >
> > equil SAM
> > &cntrl
> > ntp=1,
> > ntr=1,
> > /
> >
> > What is really curious...is that it seems that the problem occurs
> only at
> > the restart
>
> This has the hallmarks of a problem with the restraint coordinates: in
> the
> restart run, what file are you using for the -ref flag? If it is not
> the
> same file as that for the -c flag, run an experiment to see if the
> problem
> goes away when -ref and -c point to the same file.
>
> This is just a guess, but it's simple to check.
>
> ....dac
>
>
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Received on Thu Nov 10 2011 - 21:00:02 PST
