[gmx-users] COM Pulling

[Justin A. Lemkul]

On 6/29/12 9:03 AM, Raj wrote:
> HI , I have been performing SMD after reading bevan lab tutorial. The
> tutorial was very informative in basic aspects. Now I have my ligand inside
> the protein and I wan to pull it out in a specific direction. I applied
> force separately along the X, Y and Z axis . In which none of the pull seems
> to be proper. In the sense the ligand didn't come through the already
> predicted channel. So my question is can i specify the direction of the pull
> by mentioning the amino acid residues lined along the channel of the protein
> ? if i can what is the modification I should do to achieve the objection.

You can use any valid group as a reference, provided that you specify it in an 
index group when running grompp.

-Justin

-- 
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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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