[gmx-users] enegry minimisation

sonali dhindwal sonali11dhindwal at yahoo.co.in
Thu May 20 15:06:52 CEST 2010


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.

--
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> 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>/* 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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