[gmx-users] PMF and lack if NPT equilibration

[Justin Lemkul]

On 10/10/16 4:57 AM, Alex wrote:
> 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?
>

It's no different from any simulation.  You need to equilibrate under the 
ensemble you're going to use for data collection before you actually do that 
data collection.  If you would normally want NPT for a Gibbs free energy and 
can't get it for whatever reason (like the algorithmic limitation mentioned), 
then equilibrate with NPT to arrive at the desired density, and continue with 
NVT.  You won't get a Gibbs free energy, you'll get the Helmholtz free energy, 
but at least the density will be right.  Otherwise, build a bigger system that 
removes the restrictions of direction_periodic and use NPT.

-Justin

> 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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-- 
==================================================

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

==================================================