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
--
========================================
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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