[gmx-users] Pressure Coupling in GROMACS

[Jashimuddin Ashraf]

Thanks for your reply Dr. Lemkul. I came across some of the widely
fluctuating pressures before but the average pressure was more or less
close to the target values previously (even though the instantaneous values
varied quite a lot).

But in my case, the average pressure is far different from the target
values.

The pressure curve I am generating using g_energy is attached here.


PS. I have 2 carbon nanotubes in my system; one of them is entirely frozen
and the other one is entirely free. Is anything wrong with my system?

Thanks in advance.

On Mon, Jun 8, 2015 at 7:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/8/15 9:10 AM, Jashimuddin Ashraf wrote:
>
>> Dear GROMACS users,
>>
>> I am new to GROMACS. My system contains only carbon nanotubes and inside
>> my
>> md.mdp file I have-
>>
>>
>> ----------------------------------------------------------------------------------------------------------------------------
>> .
>> .
>> Pcoupl                   = berendsen
>> Pcoupltype               = isotropic
>> tau_p                    = 1            ; @pressure coupling 1ps
>> compressibility          = 4.5e-5        ;
>> ref_p                    = 1.0            ; @reference pressure
>> .
>> .
>>
>> ----------------------------------------------------------------------------------------------------------------------------
>>
>>
>> whenever I run the grompp command, I get a warning called-
>>
>>
>>
>> ----------------------------------------------------------------------------------------------------------------------------
>>
>> Using Berendsen pressure coupling invalidates the true ensemble for the
>> thermostat
>>
>> ----------------------------------------------------------------------------------------------------------------------------
>>
>> I looked up at the mail list where I found Parrinello-Rahman to be
>> appropriate for the NPT simulations. But I intend to run production MD. Is
>> this an error to be
>> worried about? (I can obviously run simulations using maxwarn)
>>
>>
> Don't confuse common jargon with more strict definitions.  Running "NPT"
> doesn't mean it's different than "production MD."  Your data collection can
> be done with any ensemble that makes sense.  NPT is an ensemble.  The
> Berendsen algorithms are generally pretty useful for quickly relaxing
> temperature/pressure to target values during initial equilibration, but
> their distributions are (as grompp says) not strictly correct statistical
> mechanical ensembles.  If you want to run under an NPT ensemble, use
> Parrinello-Rahman for data collection.
>
>  I have another problem. When I simulated carbon nanotubes with water/
>> other
>> molecules, the average pressure I observed from simulation (using g_energy
>> command) had a good agreement with the ref_p. But now the average pressure
>> becomes independent of my ref_p. This is a problem that is bugging me for
>> a
>> long time. How can I resolve this?
>>
>>
> You'll have to provide quantitative evidence of what you're talking about.
> Pressure fluctuates wildly during a simulation; see extensive previous
> discussions and notes on the wiki.
>
> -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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