[gmx-users] Umberella sampling

[Justin A. Lemkul]

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
> 

-- 
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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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