[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 23 12:09:01 CET 2009
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://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 <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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