[gmx-users] energy minimization problem

[Ming Tang]

Besides, the original .mdp file from the martini website is here:

define           =  -DPOSRES
dt               =  0.02 
nsteps           =  25000
nstxout          =  0 
nstvout          =  0
nstlog           =  100 
nstxtcout        =  100 
xtc-precision    =  10 
rlist            =  1.4 
coulombtype      =  shift 
rcoulomb         =  1.2 
epsilon_r        =  15 
vdw-type         =  shift 
rvdw-switch      =  0.9 
rvdw             =  1.2 
tcoupl           =  v-rescale 
tc-grps          =  Protein W 
tau-t            =  1.0 1.0 
ref-t            =  300 300 
Pcoupl           =  parrinello-rahman 
Pcoupltype       =  isotropic
tau-p            =  12.0
compressibility  =  3e-4
ref-p            =  1.0
refcoord_scaling =  all


-----Original Message-----
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

--
==================================================

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

==================================================
--
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-request at gromacs.org.