On 10/4/12 10:52 AM, jiang wrote:
Justin Lemkul wrote
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
Hi Justin,
I used ~20 windows to sample ~2 nm pulling. I notice that the distance
between the complex being increased during the pulling but not gradually.
At the distance of 0-1nm, there are 70 snapshots (the distance sometime
increased sometimes decreased). At the distance of 1-2nm, there are only
30 snapshots (the distance kept increasing always). At the distance more
than >3nm, the distance increased as 0.3nm of each snapshot, is it normal
and reliable?
I will assume you are using a harmonic potential (umbrella) to do the
pulling.
In this case, your observations are totally normal. When two species
interact
strongly, it is harder to pull them apart, thus the spring extends further
to
induce a larger force before displacement occurs. As the restoring forces
are
overcome, it is easier to move the pulled group through solution, so it
makes
more steady progress as the molecules are separated.
Hi Justin, it is right I am using umbrella pulling. Now here is another
hurdle in front of me: How to select the snapshots for umbrella samples?
Since the distance between two groups went higher or lower at the beginning
of the pulling. For example, during the pulling simulation, the distance
changes like:
0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .....
I suppose it doesn't matter which snapshots to be chosen, as long as the
snapshots can indicate a good spacing, the PMF result always should be same,
right?
You need reasonable spacing and sufficient sampling in each window to allow for
proper overlap of the umbrella potentials.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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