[gmx-users] enegry minimisation

[Gaurav Goel]

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://mc/compose?to=erikm@xray.bmc.uu.se>
> http://folding.bmc.uu.se/
>
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