On 5/15/15 9:32 AM, Ming Tang wrote:
Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be
reasonable according to gromacs website. So ijust kept trying 0.02ps
The time step will depend on the stability of the system, which in turn depends
on how well equilibrated it is. If reducing the time step promotes stability
during equilibration, that is the most obvious solution. After equilibrating
for a while, try increasing the time step.
-Justin
Sent from my Huawei Mobile
Justin Lemkul <jalem...@vt.edu> wrote:
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
==================================================
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
==================================================
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.