[gmx-users] PMF and lack if NPT equilibration

[Alex]

Thanks.

I used the "direction-periodic",  along with "semiisotropic" with zero
compressibility in Z direction to have also NPT equilibration in each
windows. Below is the final pressure after NPT equilibration with 1 bar
reference, I hope it would be ok?!

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   -252.127       0.66    165.053    3.15753  (bar)

Regards,
Alex


On Mon, Oct 10, 2016 at 8:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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