[gmx-users] enegry minimisation
Justin A. Lemkul
jalemkul at vt.edu
Thu May 20 13:53:12 CEST 2010
sonali dhindwal wrote:
> 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.
Well, you haven't properly defined position restraints. The default (produced
by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE." If you have for some
reason modified the topology, then maybe your approach is correct, but otherwise
your position restraints are not being applied.
I also find it very curious that such substantial changes are taking place
during a simple energy minimization. Are you sure the effects you are seeing
are not simply due to the visualization software you are using guessing the
incorrect secondary structure type? I have had that experience numerous times,
especially in the case of beta-strands. DSSP tells me that, geometrically, I
have beta-strands, but the visualization software renders coil structures.
In any case, large structural deviations during EM suggest something
fundamentally wrong with the model. Usually the changes in EM are small, since
it is performed at 0 K. Only huge forces would cause any sort of structural change.
> I also want to ask what is the meaning of fx fy and fz :
>
Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.
> ; 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 ?
>
These default values are typically quite sufficient to restrain the structure.
-Justin
> 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
> </mc/compose?to=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
> </mc/compose?to=gauravgoeluta at gmail.com>>/* wrote:
>
>
> From: Gaurav Goel <gauravgoeluta at gmail.com
> </mc/compose?to=gauravgoeluta at gmail.com>>
>
> Subject: Re: [gmx-users] enegry minimisation
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org </mc/compose?to=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
> <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
> <http://mc/compose?to=sonali11dhindwal@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
> <http://mc/compose?to=erikm@xray.bmc.uu.se>>/* wrote:
>
>
> From: Erik Marklund <erikm at xray.bmc.uu.se
> <http://mc/compose?to=erikm@xray.bmc.uu.se>>
> Subject: Re: [gmx-users] enegry minimisation
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org
> <http://mc/compose?to=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
> 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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