[gmx-users] Dubious results with NPT

Dr. Vitaly Chaban vvchaban at gmail.com
Tue Feb 25 16:19:05 CET 2014 

On Tue, Feb 25, 2014 at 3:57 PM, Michael Shirts <mrshirts at gmail.com> wrote:
> No full solutions to this problem -- I'll write a few notes.
>
> * With large systems run for relatively small amounts of time, the
> ensemble could be statistically indistinguishble from the true
> distribution even if the averages don't line up correctly. See:
>
> http://pubs.acs.org/doi/abs/10.1021/ct300688p
>
> For ways to examine the full distribution of volumes.
>
> * Parrinello-Rahman isn't quite correct in GROMACS because virial and
> kinetic energy are offset by 1/2 a step, though getting something more
> like 1.2 atm when running at 1 atm is more common.


I have been ever wondering why "1.2" and not "0.8" (from the own practice).


> * Note that with systems that are heterogeneous in direction (not
> uniform in x y and z), any errors in the pressure may be magnified.
>
> * If you have a property that changes when the pressure changes from 1
> to 5 atm, odds are that molecular simulation is not the right way to
> study it -- the force fields are not that accurate.


I believe this is not a force field problem. We calculate normal
boiling points by plotting saturated vapor pressure versus
temperature. The results are quite trustworthy. It is NVT simulation,
of course.

As the "problems" with simulated pressure (and conjugated properties)
are, to a large extent, due to a nanoscale size of the simulated
systems, it is probably worthwhile to estimate system density in
certain manner and then proceed with it in the NVT.



Dr. Vitaly V. Chaban





> On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>> in that case the average is reasonable, but you should state in the
>> manuscript that all the reported results correspond to 5.15 bar.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Tue, Feb 25, 2014 at 10:42 AM, sujithkakkat . <sujithks58 at gmail.com> wrote:
>>> Hi,
>>>
>>>   In fact the average pressure 5.15 bar was obtained  for the case where the
>>> reference pressure was 5 bar.  I had mentioned it in one of the previous
>>> mails. But still the average value is not that good.
>>>
>>>>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.
>>>
>>>
>>> Sujith.
>>>
>>>
>>> On Tue, Feb 25, 2014 at 2:29 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
>>> wrote:
>>>>
>>>> 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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