Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan.
Sorry for the inconvenience.
Next time I will keep in mind about the subject line.
I tried deleting those particular atoms where it gave the maximum force.
You said that this atom was part of a lipid. Deleting these atoms will give you
a broken structure and an unrealistic system. It should also cause grompp to
complain.
But every time a new atom with a maximum force was given in the output.
Is it fine to use to use "constraints = all-angles" in order to overcome
the Lincs warnings ?
No. LINCS warnings indicate that there is something fundamentally wrong with
your system. It likely stems from how you inserted your protein into the
lipids. Think about it. Your control lipid bilayer minimized fine. Your
protein-membrane system does not, if that is what we're still talking about.
That indicates to me that the problem is not with the lipids, the problem is
with the insertion of the protein.
Instead of genbox (which is somewhat crude), try the InflateGRO script from
Tieleman's site. I have used it many times to build nicely-packed membrane
protein systems. It takes substantially longer to build the system than with
genbox, but I think the results are more reliable.
-Justin
Thanks in advance.
Thanking you,
Pawan
On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
When replying to digests, please change the subject line to
something relevant.
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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> 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
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ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
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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
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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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