[gmx-users] enegry minimisation
Justin A. Lemkul
jalemkul at vt.edu
Thu May 20 15:16:04 CEST 2010
sonali dhindwal wrote:
> Hello Gaurav,
> when i did g_rms with structre before energy minimisation as refrence
> and strucutre after energy minimisation, it came to be around 0.02.
>
Is that backbone RMSD or does it consider all protein atoms? In either case, a
value of 0.02 indicates a very small amount of change in the protein structure,
which makes it very hard to believe that any large-scale alteration of the
secondary structure is happening.
-Justin
> --
> Sonali Dhindwal
>
>
> --- On *Thu, 20/5/10, Gaurav Goel /<gauravgoeluta at gmail.com>/* wrote:
>
>
> From: Gaurav Goel <gauravgoeluta at gmail.com>
> Subject: Re: [gmx-users] enegry minimisation
> To: jalemkul at vt.edu, "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Date: Thursday, 20 May, 2010, 5:36 PM
>
> Can you try using g_rms to compare the difference between the
> structures before and after EM.
>
> -Gaurav
>
> On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul <jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>> wrote:
> >
> >
> > 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
> </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: "sonali dhindwal" <sonali11dhindwal at yahoo.co.in
> </mc/compose?to=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>
> >> </mc/compose?to=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>
> >> </mc/compose?to=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>
> >> </mc/compose?to=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>
> </mc/compose?to=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>
> >>
> >>
> <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
> </mc/compose?to=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 </mc/compose?to=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
> </mc/compose?to=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 </mc/compose?to=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 </mc/compose?to=erikm at xray.bmc.uu.se>
> >> <http://mc/compose?to=erikm@xray.bmc.uu.se>
> >> http://folding.bmc.uu.se/
> >>
> >> -- gmx-users mailing list gmx-users at gromacs.org
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> >> -----Inline Attachment Follows-----
> >>
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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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--
========================================
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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