On 6/22/17 9:09 AM, Sergio Manzetti wrote:
I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database.
Removed all waters and non-nucleic acid molecules, and everything seems fine.
The mdp settings are:
title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define =
integrator = md
dt = 0.002
nsteps = 5000000
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
compressed-x-grps = DNA SOL NA CL
energygrps = DNA SOL NA CL
nstlist = 10
ns-type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
AMBER uses shorter cutoffs. Refer to their papers for what is correct.
tcoupl = V-Rescale
tc-grps = DNA SOL NA CL
tau-t = 0.1 0.1 0.1 0.1
ref-t = 310 310 310 310
Don't do this.
http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do
Pcoupl = No
tau-p = 1.0
compressibility = 4.5e-5
ref-p = 1.0
gen-vel = yes
gen-temp = 310
gen-seed = 173529
constraints = all-bonds
IIRC AMBER only constrains bonds to H, so again check the literature.
None of these points is likely fatal (maybe the thermostat) but you should use
correct settings. If your system is crashing with this .mdp file or the
corrected one, it's because you haven't adequately minimized and equilibrated.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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