[gmx-users] pressure dependence on volume.

[Dr. Vitaly Chaban]

To achieve what you want you need to MANUALLY set the average DENSITY
which you obtained from NPT. That is, you MANUALLY adjust box side
length in the GRO file.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> I am trying to transit from NPT to NVT.
> Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar
> pressure in NVT.
> I don't know why that happened.
>
> Was it the difference between constant pressure and constant volume heat
> capacity? But then, the thermostat should take care of that quite quickly.
> After that, N, V, and T would be same for NPT simulation and the NVT
> simulation... which means the pressure should be the same.
>
> Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses
> Berendsen barostat.
>
> Right now I'm selecting NPT frames with different volumes, and see if the
> NVT simulations continuing from those frames would give me the 1 bar
> pressure.
>
> On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/17/14 11:49 AM, Johnny Lu wrote:
>>
>>> At least for real water, a 0.2% error in volume can mean the pressure is
>>> ~30 bar when the target pressure is 1 bar.
>>> http://docs.engineeringtoolbox.com/documents/309/water-density-
>>> temperature-pressure_2.png
>>>
>>> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu <johnny.lu128 at gmail.com>
>>> wrote:
>>>
>>>  Hi.
>>>>
>>>> Mainly TIP3P water, 300K. The pressure is near 1 bar.
>>>>
>>>> A less than 1% error in volume would cause how much error in average
>>>> pressure?
>>>>
>>>>  From three npt simulations of 72 ns with Berendsen barostat, I get the
>>>> average volume is 298.5 nm^3.
>>>>
>>>> Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
>>>> deviation from this volume), I run NVT simulation that at first gives a
>>>> system that doesn't seem to be at equilibrium.
>>>>
>>>>
>> Does that time point correspond to the desired pressure?  The pressure
>> tensor is calculated from the virial and the kinetic energy, so those are
>> the quantities you should be looking at for instantaneous pressures.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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