[gmx-users] Pressure Coupling in GROMACS

[Justin Lemkul]

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

==================================================