Hello Gaurav,
Thanks for your reply,
I did position restrained enegry minimisation, and used following .mdp file for
the same
title = protein
cpp = /usr/bin/cpp ; the c pre-processor
define = -DPOSRE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
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
pbc = xyz
I included define = -DPOSRE, for restraining the atom postion,
I used posre.itp which was genertaed by pdb2gmx.
Have I done it correctly, because after this also many of the beeta sheets have
become short, forming loops.
I also want to ask what is the meaning of fx fy and fz :
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
11 1 1000 1000 1000
12 1 1000 1000 1000
15 1 1000 1000 1000
18 1 1000 1000 1000
19 1 1000 1000 1000
20 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
23 1 1000 1000 1000
which is there in posre.itp file, and if these should have value of 1000 1000
1000 each ?
Thanks in advance.
--
Sonali Dhindwal
--- On Wed, 19/5/10, Gaurav Goel <gauravgoel...@gmail.com> wrote:
From: Gaurav Goel <gauravgoel...@gmail.com>
Subject: Re: [gmx-users] enegry minimisation
To: "sonali dhindwal" <sonali11dhind...@yahoo.co.in>
Date: Wednesday, 19 May, 2010, 8:39 PM
For position restraints you need to do the following:
1. define a name.itp file which looks like:
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
.......
.......
_____
1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual.
2. Add "define = -Dname" to your mdp file
3. Add following lines to your topology file
; Include Position restraint file
#ifdef name
#include "name.itp"
#endif
4. compile and run.
I'm sure you will find mroe information on position-restrain simulation on
gmx-users archive.
-Gaurav
On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal
<sonali11dhind...@yahoo.co.in> wrote:
Hello Gaurav,
Can you please help me in suggesting where should I look for providing
parameters to constrain the protein backbone and then do EM and then how to run
a short MD simulation by constraining the protein backbone.
Sorry to bother you, but as I am new to Gromacs, your help will be highly
appreciable.
Thanks in advance
--
Sonali Dhindwal
--- On Wed, 19/5/10, Gaurav Goel <gauravgoel...@gmail.com> wrote:
From: Gaurav Goel <gauravgoel...@gmail.com>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Wednesday, 19 May, 2010, 6:44 PM
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.
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
-Gaurav
On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal <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> wrote:
From: Erik Marklund <er...@xray.bmc.uu.se>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <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?
-- -----------------------------------------------
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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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