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

[Pawan Kumar]

Hello Justin Sir,

Greetings from Pawan.
Sorry for the late reply.
The max. force was 1.2447973e+o5 on atom 19448.
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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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