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<div>Funny,</div>
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<div>I could but dont have time. You should look at Uni Washington things...if your doing that I would say restrain one for 10 sims, then the other and see if there's differences, and publish something on differences for restraints...on A vs. B, which I have never seen...</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 10. Februar 2015 um 03:00 Uhr<br/>
<b>Von:</b> "Justin Lemkul" <jalemkul@vt.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] Umbrella Sampling and histograms smoothness</div>
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<br/>
On 2/9/15 8:55 PM, Agnivo Gosai wrote:<br/>
> Dear Users<br/>
><br/>
> Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating<br/>
> the topology and the itp files. Therein , automatic position restraints are<br/>
> generated. Now, I have never used manual restrain force constants.<br/>
><br/>
<br/>
If you're using the pull code, yes you are. There's a force constant associated<br/>
with the spring that is applying the umbrella (harmonic) potential. If that's<br/>
not clear, stop everything you're doing and read every paper and book chapter<br/>
you can find so you understand what you're doing rather than just typing in what<br/>
a tutorial said.<br/>
<br/>
> Could any user suggest any source / literature for choosing "restraint<br/>
> forces" for DNA/protein systems ?<br/>
><br/>
<br/>
There is a wealth of information on umbrella sampling, steered MD, etc. Google<br/>
will show you in seconds.<br/>
<br/>
> Regarding window setup, is it the spacing of the windows ?<br/>
><br/>
<br/>
Possibly.<br/>
<br/>
> Except for simulation time is there any other method for increasing<br/>
> sampling ?<br/>
><br/>
<br/>
Time is the primary issue here (as in most any simulation).<br/>
<br/>
-Justin<br/>
<br/>
--<br/>
==================================================<br/>
<br/>
Justin A. Lemkul, Ph.D.<br/>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br/>
<br/>
Department of Pharmaceutical Sciences<br/>
School of Pharmacy<br/>
Health Sciences Facility II, Room 629<br/>
University of Maryland, Baltimore<br/>
20 Penn St.<br/>
Baltimore, MD 21201<br/>
<br/>
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
<a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br/>
<br/>
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