[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 21 13:38:12 CET 2009
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.
> Thanks for your suggestions and help.
> Thanking you,
> 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
> > 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
> 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.
> > 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
jalemkul[at]vt.edu | (540) 231-9080
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