[gmx-users] enegry minimisation

[Justin A. Lemkul]

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 
> <sonali11dhindwal at yahoo.co.in <mailto: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
>     <mailto:erikm at xray.bmc.uu.se>>/* wrote:
> 
> 
>         From: Erik Marklund <erikm at xray.bmc.uu.se
>         <mailto:erikm at xray.bmc.uu.se>>
>         Subject: Re: [gmx-users] enegry minimisation
>         To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
>         <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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