[gmx-users] MDP for DNA with ions

[Justin Lemkul]

On 6/22/17 8:56 AM, Sergio Manzetti wrote:
> HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the DNA system won't minimize .
> 
> What is your experience with DNA simulations and these settings? Do you have an mdp file that may be generally good for DNA sims?
> 

Settings depend on the force field, not the molecules in the system.  If you 
want commentary, please provide a full .mdp file, not just select settings.

-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

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