[gmx-users] 0 +- 0.5 bar ok?
jalemkul at vt.edu
Tue Dec 16 13:41:14 CET 2014
On 12/15/14 11:01 AM, Johnny Lu wrote:
> Are these pressures acceptable for reviewers? (I haven't submit anything to
> journals before). What would be different from a simulation with a truly 1
> bar average pressure?
> System 1: NVT simulation gives an 0.0 +- 0.5 bar average pressure over
> 600ns with 2 fs timestep. When I averaged the 2nd half of the simulation,
> it gives -0.3 +- 0.5 bar average pressure over 300 ns. The system has 9K
> water molecules, 3 Cl- ions, and 173 amino acid residues (2598 atoms).
> System 2: Another simulation that i did was an alanine dipeptide simulation
> with a 5.4 +- 0.2 bar pressure over 250 ns. The last 150 ns gives an
> average pressure of 5.6 +- 0.2 bar. The system has 8k water molecules and
> 32 peptide atoms.
People never report such details unless it is critical to the interpretation of
the results. As presented here, I have no idea if it's meaningful. Under NVT,
pressure is going to be based on your enforced box dimensions; it's not usually
a useful quantity.
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
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