Hello Justin Sir,<br><br>Greetings from Pawan.<br>Sorry for the inconvenience.<br>Next time I will keep in mind about the subject line.<br>I tried deleting those particular atoms where it gave the maximum force.<br>But every time a new atom with a maximum force was given in the output.<br>
Is it fine to use to use "constraints = all-angles" in order to overcome the Lincs warnings ?<br>Thanks in advance.<br><br>Thanking you,<br>Pawan<br><br><br><br><br><div class="gmail_quote">On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
When replying to digests, please change the subject line to something relevant.<br>
<br>
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello Justin Sir,<br>
<br>
Greetings from Pawan.<br>
Sorry for the late reply.<br>
The max. force was 1.2447973e+o5 on atom 19448.<br>
</blockquote>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
This particular atom belongs to one of the lipid residues of the bilayer.<br>
I get Lincs warnings whenever I run the position restraint mdrun.<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
<br>
On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Pawan Kumar wrote:<br>
<br>
Hello Justin Sir,<br>
<br>
Greetings from Pawan<br>
Thanks for your valuable suggestion and reply.<br>
Initially I gave the emtol of 1000 and the output I got was :<br>
Steepest Descents converged to machine precision in 163 steps<br>
but did not reach the requested Fmax<1000.<br>
Potential Energy = - 4.4516497e+05<br>
<br>
<br>
...and how close did Fmax get to 1000?<br>
<br>
<br>
Even I tried to minimize the popc bilayer which I took from<br>
Tieleman sir's website ( before generating a bigger bilayer<br>
using genconf ) but that also converged to machine precision but<br>
not to the requested Fmax<1000. How do I proceed further ?<br>
<br>
<br>
Well, these things are not absolute; Fmax = 1000 is kind of a rule<br>
of thumb that I use in my own work, but sometimes it is not<br>
necessary. Careful equilibration should massage your system into<br>
cooperating.<br>
<br>
-Justin<br>
<br>
Thanks for your suggestions and help.<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
On Thu, Mar 19, 2009 at 9:13 PM,<br>
<br>
Pawan Kumar wrote:<br>
> Hello Justin Sir,<br>
><br>
> Greetings from Pawan<br>
> Thanks for your valuable suggestion and reply.<br>
> After inserting the protein in the bilayer using genbox I have<br>
minimized<br>
> the whole system without using any position restraints<br>
(i.e. define =<br>
> -DFLEXIBLE in em.mdp file). I used vanderwaal's distance<br>
parameter (<br>
> -vdwd of 0.6 ) in the genbox step.<br>
> After running mdrun for energy minimization I got the<br>
output as :<br>
> Steepest Descents converged to Fmax<2250 in 14 steps.<br>
> Potential energy = - 6.9484700e+05<br>
> Maximum force = 2.2114819e+03 on atom 34277<br>
> Norm. of force = 5.0103039e+04<br>
><br>
<br>
You should try for an Fmax of no greater than 1000. 2250 is<br>
still<br>
very high.<br>
<br>
> I tried decreasing the emtol value in the em.mdp file but it<br>
ended with<br>
> machine precision.<br>
<br>
How far did it converge? What was Fmax?<br>
<br>
> I have read in literature that 5000 steps of Steetest<br>
Descents run is<br>
> required after inserting the protein in the bilayer which<br>
should be<br>
> followed by atleast 1000 steps of conjugate gradients. How<br>
can I<br>
> accomplish this ? Is there any parameter to be given in the<br>
em.mdp file<br>
> ? I use steep as the integrator in the mdp file for energy<br>
minimization.<br>
<br>
Read the manual.<br>
<br>
Whether or not that exact setup is going to be "required" is<br>
likely<br>
system-specific. I would say that as long as your system<br>
converges<br>
to a stable,<br>
negative Epot with a reasonable Fmax (less than 1000, but ideally<br>
lower) then<br>
you *may* have an appropriate starting structure.<br>
<br>
-Justin<br>
<br>
> Please help with some suggestions.<br>
> Thanks in advance.<br>
><br>
> Thanking you,<br>
> Pawan<br>
><br>
><br>
><br>
<br>
<br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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