AMBER Archive (2009)
Subject: Re: [AMBER] unexplained blow-up at restart
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jul 13 2009 - 05:24:23 CDT
try loading both the inpcrd and refc into a program like vmd, it might help
to see if they are shifted, or if somehow the coordinates got wrapped around
the periodic box, etc
On Mon, Jul 13, 2009 at 3:01 AM, Sally Pias <sallypias_at_gmail.com> wrote:
> For the record, setting nscm to 0 did not solve the problem of
> extremely high restraint energy on restart (though I do think keeping
> nscm at 0 with positional restraints is probably important). I was
> able to restart successfully by using the end coordinates of the
> previous run as the reference coordinates, rather than the coordinates
> of the structure prior to MD. I found the following reflector
> discussion helpful in this regard:
> http://archive.ambermd.org/200703/0071.html (subject line:
> "coordinate changes using ptraj").
> On Fri, Jul 10, 2009 at 12:59 PM, Sally Pias<sallypias_at_gmail.com> wrote:
> > Carlos,
> > It sounds like you may have identified the problem, as the only thing
> > I noticed in visualizing the md2_NPT trajectory is that the molecule
> > shifts over (translates) noticeably at step 1. That is why I tried
> > the Langevin thermostat, as I thought it might be a "flying ice cube"
> > effect. I will try setting ntcm to 0.
> > Many thanks,
> > Sally
> > On Fri, Jul 10, 2009 at 11:58 AM, Carlos
> > Simmerling<carlos.simmerling_at_gmail.com> wrote:
> >> Sally- I got your files.
> >> can you redo rune after changing ntcm to 0, and also try switching back
> >> Berendsen thermostat (ntt=1)?
> >> try them separately. it may be that in run2 the molecule was recentered,
> >> the refc was not. in general combining positional restraints with
> removal of
> >> center of mass motion can be dangerous. we have better checks in more
> >> versions of Amber
> >> carlos
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