[gmx-users] PMF and lack if NPT equilibration

[Alex]

Thanks for your response.

My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.

You means in the step six of the tutorial no necessarily need to do any NVT
or NPT before production simulation?

Thanks,
Alex


On Mon, Oct 10, 2016 at 2:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/8/16 2:46 PM, Alex wrote:
>
>> Dear gromacs user,
>>
>> In a PMF simulation of a short peptide on solid surface, I am using the
>> "direction-periodic" as "pull-coord1-geometry" in the Z  direction, then
>> as
>> you know the equilibration of the system in NPT ensemble is not doable for
>> the individual windows. So, for each windows of umbrella sampling, I am
>> going to do minimization and NVT equilibration and then MD production. I
>> was wondering if the lack of the NPT  equilibration would not badly affect
>> on the result PMF? If so, how can I compensate it somehow?
>>
>>
> All you're doing is sampling under a different ensemble.  There's no
> reason to think that a PMF requires an NPT ensemble.
>
> -Justin
>
> By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
>> of production simulation of my initial system before coming to the pulling
>> step.
>>
>> Thanks.
>>
>> Regards,
>> Alex
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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