[gmx-users] Re: g_mindist - reg

[Justin Lemkul]

On 9/3/12 7:47 AM, Raj wrote:
> thank you justin ... I have given the entire protein as one group.. now will
> it be ok or i need to give only hydrophobic resides alone as a index group.
> Thank you once again for yor response
>
>

If you want hydrophobic contacts, you need index groups that specify hydrophobic 
atoms, otherwise you're getting all contacts - polar and nonpolar - in the 
calculated quantity.

-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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