[gmx-users] enegry minimisation

sonali dhindwal sonali11dhindwal at yahoo.co.in
Thu May 20 13:44:51 CEST 2010


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 <gauravgoeluta at gmail.com> wrote:

From: Gaurav Goel <gauravgoeluta at gmail.com>
Subject: Re: [gmx-users] enegry minimisation
To: "sonali dhindwal" <sonali11dhindwal at 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 <sonali11dhindwal at 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 <gauravgoeluta at gmail.com> wrote:


From: Gaurav Goel <gauravgoeluta at gmail.com>

Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users at 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 <sonali11dhindwal at 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 <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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