[gmx-users] trajectory analysis

[Justin A. Lemkul]

On 6/5/12 4:40 AM, Turgay Cakmak wrote:
>
> Hi all,
>
>
> I would like to get information about *pi-pi stacking*, *van der Waals*,
> *electrostatic and hydrophobic interactions* for my system (several-peptides in
> a box filled with water). Can Gromacs compute these interactions?
>
>
> As far as I see from mailing-list, to get information on *hydrophobic
> interactions*, g_mindist and g_sas can be used. But, they look very different.
> Which one should be used?
>

Both.  There are no Gromacs tools that magically do the analysis you're looking 
for, but combinations of available tools will.  You can use g_mindist with a 
suitable index group to find hydrophobic contacts, and g_sas to compute 
hydrophobic and polar surface area.  Other tools that can be useful for your 
other metrics are g_hbond, g_dist, and others.  See the manual for a complete 
listing and decide what might be useful based on what you read there.

-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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