[gmx-users] Umbrella Sampling and histograms smoothness

[Justin Lemkul]

On 2/9/15 8:55 PM, Agnivo Gosai wrote:
> Dear Users
>
> Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating
> the topology and the itp files. Therein , automatic position restraints are
> generated. Now, I have never used manual restrain force constants.
>

If you're using the pull code, yes you are.  There's a force constant associated 
with the spring that is applying the umbrella (harmonic) potential.  If that's 
not clear, stop everything you're doing and read every paper and book chapter 
you can find so you understand what you're doing rather than just typing in what 
a tutorial said.

> Could any user suggest any source / literature for choosing "restraint
> forces" for DNA/protein systems ?
>

There is a wealth of information on umbrella sampling, steered MD, etc.  Google 
will show you in seconds.

> Regarding window setup, is it the spacing of the windows ?
>

Possibly.

> Except for simulation time is there any other method for increasing
> sampling ?
>

Time is the primary issue here (as in most any simulation).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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