[gmx-users] trajectory analysis

[Turgay Cakmak]

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
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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