Gavin Melaugh wrote:
Hi all
Could someone please get back to me on this. I have ran two sets of
umbrella sampling simulations
1- Using pull_geometry = distance, and pull_dim = Y Y Y
2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
0.735968
In both cases I wish to calculate the PMF for taking a host out of a
guest. I specify the distance between the COM of the two groups in the
respective mdp files. The two curves I get are completely different
which has leads me to ask a couple of questions:
You're doing two different things here, so I'd suspect that you're going to get
a different answer with different settings.
1) Does the vector change as the dynamics evolves (i.e is it just
relative between the two points) or does it remain fixed in space?
It is relative.
2) Using umbrella sampling in the second case does the relative position
of the pull group (guest) fluctuate about the distance along the
specified vector?
Yes.
Note- I couldn't run g_wham with pull_geometry = direction in my current
version of gromacs, so I ran it in 4.5.3 but I had to use the -if
pullf-files.xvg option.
We'll have to assume that your "current version" is something in the 4.0.x
series, so this outcome is expected.
http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force
Some help would be appreciated as I have to be sure of what the program
is actually doing.
There's always the code :)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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