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Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan.
Sorry for the late reply.
The max. force was 1.2447973e+o5 on atom 19448.
An Fmax that high is sure to generate problems. It is up to you to inspect your
system, understand which atoms are interacting to cause such a force, and
determine if you've done something wrong.
-Justin
This particular atom belongs to one of the lipid residues of the bilayer.
I get Lincs warnings whenever I run the position restraint mdrun.
Thanking you,
Pawan
On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan
Thanks for your valuable suggestion and reply.
Initially I gave the emtol of 1000 and the output I got was :
Steepest Descents converged to machine precision in 163 steps
but did not reach the requested Fmax<1000.
Potential Energy = - 4.4516497e+05
...and how close did Fmax get to 1000?
Even I tried to minimize the popc bilayer which I took from
Tieleman sir's website ( before generating a bigger bilayer
using genconf ) but that also converged to machine precision but
not to the requested Fmax<1000. How do I proceed further ?
Well, these things are not absolute; Fmax = 1000 is kind of a rule
of thumb that I use in my own work, but sometimes it is not
necessary. Careful equilibration should massage your system into
cooperating.
-Justin
Thanks for your suggestions and help.
Thanking you,
Pawan
On Thu, Mar 19, 2009 at 9:13 PM,
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
>
>
>
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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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