[gmx-users] Re: Re: Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:

> I have a test set which is comprised of the same constituents of my real 
> system, except the solvent (i mean, it is in vacuum. This test set I use 
> to (as the name says) test different different parameters without having 
> to wait too much. I know it would not serve as a very quantitative set, 
> but even though, when I changed the force_constant of the umbrella 
> potentia to a lower value (from 35 to 10) I got something out of the 
> WHAM that looked more like a "rollercoaster", I little bit edgy perhaps, 
> but at least not a downstream line like the one before. When I changed 
> it again to 5 kJ, the graphic still looked like a rollercoaster but it 
> differed in 1 or 2 kcal more negative than the one with 10 kJ as 
> umbrella force constant. Perhaps, in addition to space my intervals as a 
> function of distance, my spring constant is wrong. Does that make any sense?

Well, a "vacuum" run might be a bit strange, anyway, so I wouldn't base much on 
it, since the force fields weren't designed for that kind of usage.  Rough edges 
and transitions might be present, but could be smoothed with proper sampling and 
window distribution.  As for the force constant, I generally see much greater 
numbers in the literature (500-1000 kJ mol^-1 nm^-2).  I don't know if there's a 
rule of thumb for assigning this value.

> Ahh...by the way, the link for oldwiki is not working. I will try it later.
> 

Indeed, it has been running very slowly, at least.  You can access the same 
content here:

http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive

-Justin

> 
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-- 
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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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