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.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.gmail.com> wrote:
>> Sally- I got your files.
>> can you redo rune after changing ntcm to 0, and also try switching back to
>> Berendsen thermostat (ntt=1)?
>> try them separately. it may be that in run2 the molecule was recentered, and
>> 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 recent
>> versions of Amber
>> carlos
>
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Received on Mon Jul 13 2009 - 01:09:25 PDT
