[gmx-users] Simulations in NVE ensemble with CHARMM36

Justin Lemkul jalemkul at vt.edu
Wed May 7 19:08:03 CEST 2014

On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:
> Dear GMX-users
> I have done a 90 ns long simulation of a heterogeneous  system (SPCE water, phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with GROMACS4.6.5. to compute related dynamical properties, I would like to continue this simulation in NVE. But I am puzzled to choose the mdp parameters to have a good energy conservation. Indeed, I have checked the gromacs 2004 JCTC or the following and follow the advices given in the following threads
> http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
> https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html
> But I always obtain for my system a large drift and the temp decreases significantly (20 K) after few dozens of ps (the initial temp was around 297.3 K). For this simulation I used the double precision of gromacs with a timestep of 1 fs.

Can you provide a full .mdp file so we can look at all your settings?  Are these 
drifts during NPT or NVE?

> More, since I have never used the potential-modifier features, so I not sure how to setup  the correct parameters in the context of CHARMM simulations.

With the caveat that I have NOT thoroughly tested the following, my 
understanding of the new Verlet options indicates that these settings should 
perform pretty well using CHARMM36:

cutoff-scheme = Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2

Again, barely tested on my part, and never tested for NVE.



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


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