The restart coordinates (input for the second NPT run) look fine. The
protein has simply translated a couple of Angstroms, in comparison to
the reference coordinates (structure prior to MD). Otherwise, the
structures are nearly identical. Note that the restart coordinates
are from a run with nscm set to 0.
On Mon, Jul 13, 2009 at 4:24 AM, Carlos
Simmerling<carlos.simmerling.gmail.com> wrote:
> 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.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.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 - 10:11:00 PDT
