[gmx-users] enegry minimisation

[sonali dhindwal]

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 [4]
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
Thanks
--
Sonali Dhindwal

--- 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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