> On Nov 12, 2014, at 7:15 AM, David A Case <case.biomaps.rutgers.edu> wrote:
>
> On Tue, Nov 11, 2014, ZHAO Ruisheng wrote:
>
>> Thanks for your reply. This thim , I did the heating in serial
>> mode, and there is a error message (vlimit exceeded for step
>> 0; vmax = 20.1728). Moreover, the potential energy at the
>> beginning of MD (-15181) doesn't matches that at the end of
>> minimization (-13176),but for the examples of amber tutorial
>> (http://ambermd.org/tutorials/basic/tutorial1/section5.htm), the
>> potential energy at beginning of MD (-44677) doesn't match that at the
>> end of minimization (-41777) though.
>
> I'm not sure what is going on with the tutorial, but you will need to fix
> this for your problem. The force field and related parameters for the
> minimization and dynamics need to be the same. Look carefully at all the
> input parameters, and at the components of the energy to see if you can
> isolate the differences.
I agree with this assessment in general. The one exception I’ll grant here is that you might be using different restraints in the minimization compared to the heating stage. So it’s possible that the RESTRAINT contribution will be different (if, for example, you weaken the restraints from the minimization to heating stages as I often do; or if you eliminate the restraints when heating altogether).
The rest of the potential energy contributions should line up, as Dave mentioned.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 12 2014 - 05:00:06 PST
