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