[gmx-users] energy minimization problem
m21.tang at qut.edu.au
Fri May 15 04:17:10 CEST 2015
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
nsteps = 50000
nstxout = 0
nstvout = 0
nstlog = 1000
nstxtcout = 1000
xtc-precision = 10
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
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-users at 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 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
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