[gmx-users] Dubious results with NPT

[Dr. Vitaly Chaban]

your average pressure is the pressure you should report in the
publication. if you got 5 bars instead of 1 bar, you should write

"I simulated the system at 5 bars"


Dr. Vitaly V. Chaban


On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . <sujithks58 at gmail.com> wrote:
> On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat . <sujithks58 at gmail.com>
> wrote:
>> Hello,
>>
>>   Thank you both for  the comments. I am using gromos96 forcefield . I
>> read
>> a little bit  and as you said the nonbonded cutoff has to be higher.
>> The tau_p=5ps was chosen , since the manual mentions that the value has to
>> be raised by 4-5 times on going from berendsen to parrinello-rahman
>> barostat, though I did not completely follow the reasons behind it. I will
>> try with lower values.
>>
>>    I had run an earlier simulation with the same parameters for a pure
>> water
>> system for 5ns and reference pressure 5bar, and things worked fine there
>> with the average pressure at 5.15bar.
>
>
> No, this average pressure is not fine.
>
>
>
>  Why isn't it fine? I admit it is not very good. I guess due to huge
> fluctuations the average pressure is tend to vary a bit to either side of
> the reference value, unless I continue the equilibration for a very long
> time. Also the average was calculated with g_energy, which I guess
> considered the entire simulation, where the first few time steps, when the
> system is away from equilibrium,  would have poor pressure values with
> respect to reference , which would reflect in the average pressure
> calculated.
> Also using g_analyze to calculate average pressure between different times
> during the simulation did not give the same value.  So I am not sure if I
> should aim at an average pressure which is equal to the reference pressure.
>
> Thanks,
> Sujith.
>
>
>
> On Mon, Feb 24, 2014 at 4:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 2/23/14, 11:37 PM, sujithkakkat . wrote:
>>>
>>> Hello,
>>>
>>>    Thank you both for  the comments. I am using gromos96 forcefield . I
>>> read
>>> a little bit  and as you said the nonbonded cutoff has to be higher.
>>> The tau_p=5ps was chosen , since the manual mentions that the value has
>>> to
>>> be raised by 4-5 times on going from berendsen to parrinello-rahman
>>> barostat, though I did not completely follow the reasons behind it. I
>>> will
>>> try with lower values.
>>>
>>>     I had run an earlier simulation with the same parameters for a pure
>>> water system for 5ns and reference pressure 5bar, and things worked fine
>>> there with the average pressure at 5.15bar. I guess the sigma  for the
>>> case
>>> of water was low and therefore the small cut-off of 0.8nm did not matter.
>>> However the case of cyclohexane alone remains to be tried.
>>>
>>> I guess Dr Vitaly was saying about using a switch/shift function.
>>> I will try the simulation with the new settings and see.
>>>
>>
>> The Gromos force fields were parametrized with a plain cutoff for van der
>> Waals.  They do not require switching or shifting.  It's true that plain
>> cutoffs are a bit harsh, but switching and shifting have their own issues,
>> and one should always stick to the parametrization methods unless there is
>> demonstrable evidence that the new method is better.  I have never known
>> Gromos96 force fields to need anything other than plain cutoff for van der
>> Waals to function as expected.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>