mohsen ramezanpour wrote:
Dear All And Specially Dear Justin
I read the toturial of Umbrella Sampling.It was very useful
But there are afew question,of course about my work .
1-Is it necessary pulling one molecule along the line connecting their
COMs?
The pull code is based on COM distances, so in a basic sense, yes. But you
don't necessarily have to have two entire molecules as your pull and reference
groups; you can pull on a specific residue of one or the other, etc.
Another type of PMF would be a dihedral rotation curve, so in a broad sense, PMF
is not necessarily a linear calculation, but rather one that is carried out over
a generic coordinate.
2-I have a protein-drug complex,it has oriented in a ordinary direction
in 3D space
How can I say Gromacs to pul drug along that line?
See the pull_vec1 .mdp option.
in the other words,are there any way to rotate system to an special
direction?
You can use editconf -rotate, but any arbitrary orientation can be utilized.
-Justin
thanks in advance for your guides.
Mohsen
--
========================================
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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