[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

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

I tried decreasing the emtol value in the em.mdp file but it ended with
machine precision.
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. 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
> >      >
> >      >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
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> --
> ========================================
>
> 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
>
> ========================================
>
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