On 5/14/15 10:02 PM, Ming Tang wrote:
Hi Justin
Here is the .mdp file with position restraints, which I downloaded from the
martini tutorial website. It works well with the tutorial and my small triple
helix, and the grompp process does not give any warnings. Please help to have a
look. Many thanks to you.
define = -DPOSRES
integrator = md
dt = 0.02
Have you tried simply reducing the time step? 20 fs may be reasonable for a
well equilibrated system, but if the run is dying early, then this is the first
thing I would look at.
-Justin
nsteps = 50000
nstxout = 0
nstvout = 0
nstlog = 1000
nstxtcout = 1000
xtc-precision = 10
cutoff-scheme =verlet
coulombtype = reaction-field-zero
coulomb-modifier = potential-shift-verlet
rcoulomb-switch = 0.9
rcoulomb = 1.4
epsilon_r = 15
vdw-modifier = force-switch
rvdw-switch = 0.9
rvdw = 1.4
tcoupl = v-rescale
tc-grps = Protein W
tau-t = 1.0 1.0
ref-t = 310 310
compressibility = 3e-4
ref-p = 1.0
refcoord_scaling = all
pbc = xyz
-----Original Message-----
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/14/15 9:47 PM, Ming Tang wrote:
Dear Justin,
I saw it in the terminal.
Potential Energy = -6.3682131e+05
Maximum force = 1.8876091e+02 on atom 1147
Norm of force = 3.1155257e+00
But, how can I further minimize my protein?
Minimization is not your problem. Post a full .mdp file of the run that is
failing.
-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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==================================================
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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