[gmx-users] Doubt regarding membrane protein in POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 19 14:04:42 CET 2009
Pawan Kumar wrote:
> Hello Justin Sir,
>
> Greetings from Pawan
> Thanks for your valuable suggestion and reply.
> After inserting the protein in the bilayer using genbox I have minimized
> the whole system without using any position restraints (i.e. define =
> -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter (
> -vdwd of 0.6 ) in the genbox step.
> After running mdrun for energy minimization I got the output as :
> Steepest Descents converged to Fmax<2250 in 14 steps.
> Potential energy = - 6.9484700e+05
> Maximum force = 2.2114819e+03 on atom 34277
> Norm. of force = 5.0103039e+04
>
You should try for an Fmax of no greater than 1000. 2250 is still very high.
> I tried decreasing the emtol value in the em.mdp file but it ended with
> machine precision.
How far did it converge? What was Fmax?
> I have read in literature that 5000 steps of Steetest Descents run is
> required after inserting the protein in the bilayer which should be
> followed by atleast 1000 steps of conjugate gradients. How can I
> accomplish this ? Is there any parameter to be given in the em.mdp file
> ? I use steep as the integrator in the mdp file for energy minimization.
Read the manual.
Whether or not that exact setup is going to be "required" is likely
system-specific. I would say that as long as your system converges to a stable,
negative Epot with a reasonable Fmax (less than 1000, but ideally lower) then
you *may* have an appropriate starting structure.
-Justin
> Please help with some suggestions.
> Thanks in advance.
>
> Thanking you,
> Pawan
>
>
>
> On Thu, Mar 19, 2009 at 5:41 PM,
>
> Pawan Kumar wrote:
> > Hello Justin Sir,
> >
> > Thanks for your reply.
> > I changed the dt value as per the suggestion.
> > But after 200 steps the same kind of warnings came like "pressure
> > scaling more than 1%" and "1-4 interactions" and then it stopped
> after
> > writing few pdb files. Then I decreased the dt value still lesser
> > (0.00001) and this time it continued with all the given steps but the
> > lipids' structure were distorted into small fragments.
>
> If your system is not properly energy-minimized, there is no change
> in dt that
> will help you. Ensure that your EM converged to reasonable values
> of Epot and
> Fmax before continuing.
>
> > The other query I have is what should the optimal value for these
> > parameters for membrane proteins : rlist, rcoulomb, and rvdw. I have
> > used the value of 1 before.
>
> These parameters depend upon the force field you are using. Read
> about the
> parameter set, as well as modifications that may be made to it.
> Studies have
> suggested that longer cut-off's should be used with membrane
> proteins. There is
> no substitute for a thorough literature search before starting a
> project!
>
> > One last question is how to overcome the lincs warnings in position
> > restraint mdrun.
>
> That will depend upon whether or not your system is properly
> constructed and
> energy-minimized.
>
> -Justin
>
> > Thanks in advance.
> >
> > Thanking you,
> > Pawan
> >
> > On Thu, Mar 19, 2009 at 5:01 PM,
> >
> > Pawan Kumar wrote:
> > > Hi Xavier sir,
> > >
> > > Thanks for your valuable reply.
> > > How can I refine the non-bonded set-up ?
> >
> > rlist, rcoulomb, rvdw as well as coulombtype. *Never* use
> cut-off
> > electrostatics for a membrane system (or really any other,
> for that
> > matter).
> > Your results will be far less accurate than with PME (this is
> in the
> > literature).
> >
> > > And where can I specify the time step to 0.0001 ?
> >
> > dt (read the manual).
> >
> > -Justin
> >
> > > I am new to gromacs.
> > > Sorry to ask such questions.
> > >
> > > Thanking you,
> > > Pawan
> > >
> > >
> >
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
>
> End of gmx-users Digest, Vol 59, Issue 137
> ******************************************
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list