[gmx-users] enegry minimisation
Gaurav Goel
gauravgoeluta at gmail.com
Wed May 19 15:29:33 CEST 2010
On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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, thanks for clarifying. I was referring to position restraints.
-Gaurav
> -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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