Thank you for your reply. I will read the manual more carefully. 2012/6/5 Justin A. Lemkul <[email protected]>
> > > 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> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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