[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/13/15 5:00 PM, shivangi nangia wrote:
> Hello All,
>
> Thank you all for you input.
>
> I now have access to GROMACS 5.0.
>
> On using the recommended settings, the APL is sill dropping within 3 ns of
> the simulation.

3 ns is orders of magnitude too short to draw any conclusions.  Simulate out to 
100 ns and we'll talk :)  I only say this because I know the APL can be 
reproduced with the settings I gave in CHARMM and GROMACS with very close agreement.

<snip>

> nstlist                  = 1

Yikes!  You're losing a ton of performance here (though check the log to make 
sure Verlet adjusted this to something more suitable).  Setting nstlist = 1 is 
only for energy minimization.

-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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