[gmx-users] enegry minimisation
sonali11dhindwal at yahoo.co.in
Wed May 19 14:18:31 CEST 2010
Sorry, but I couldnt get your question,
I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field :
title = drg_trp
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson’s Flexible water model 
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01
I hope it will help you to guide me further
--- On Wed, 19/5/10, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
From: Erik Marklund <erikm at xray.bmc.uu.se>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, 19 May, 2010, 5:31 PM
sonali dhindwal skrev:
> Hello All
> This question may sound trivial to many, but as i am new to this field, please help.
> I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation.
> I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs.
> So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I have done refinement also.
> Thanks and regards
> Sonali Dhindwal
So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME?
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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