[gmx-users] umbrella potential

[Berk Hess]

You should also be aware that when you determine a PDF for a distance
constrained in 3D, you will always get a "trivial" entropy contribution
of -2 kT log(r), which will eventually make all curves tend downwards.

Berk

> Date: Sun, 20 Sep 2009 20:28:02 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] umbrella potential
> 
> 
> 
> Stefan Hoorman wrote:
> > I have performed a series of umbrella sampling simulations in order to 
> > do a WHAM analysis. The profile.xvg file I obtain is a continuous 
> > descending line along my distance axis. There is no increase in energy 
> > after my two structures separate. Perhaps I am doing something wrong.
> 
> Sounds like it, but there's no way anyone on this list will know that unless you 
> describe your system in greater detail - how you generated the starting 
> configurations, how many windows you used and what distances that corresponds 
> to, the pull parameters you've specified in your .mdp file, and anything else 
> that might be pertinent.
> 
> -Justin
> 
> > Thank you
> > 
> > 
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> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> 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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