Gaurav Goel wrote:
After adding water you can do energy minimization (EM) in two steps:
1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.
The above three steps will help hydrate the protein molecule with
minimal distortion of protein structure.
Such finesse may certainly be beneficial. Just for clarity, though, what you
are referring to is the application of (position) restraints, not constraints.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
-Justin
4. Now run a MD on full system.
for details looks here:
http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ
<http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ>
-Gaurav
On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
<sonali11dhind...@yahoo.co.in <mailto:sonali11dhind...@yahoo.co.in>> wrote:
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 /<er...@xray.bmc.uu.se
<mailto:er...@xray.bmc.uu.se>>/* wrote:
From: Erik Marklund <er...@xray.bmc.uu.se
<mailto:er...@xray.bmc.uu.se>>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org
<mailto:gmx-users@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?
-- -----------------------------------------------
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Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
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--
========================================
Justin A. Lemkul
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Virginia Tech
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