[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138

[Justin A. Lemkul]

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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-- 
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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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