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
> >
> >
>
>
>
>
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--
========================================
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
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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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