[gmx-users] trajectory analysis
turgaycakmak34 at gmail.com
Tue Jun 5 12:34:54 CEST 2012
Thank you for your reply. I will read the manual more carefully.
2012/6/5 Justin A. Lemkul <jalemkul at vt.edu>
> 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
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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