[gmx-users] computing contacts

[David van der Spoel]

On Mon, 2005-01-17 at 16:42 +0100, Luca Mollica wrote:
> Dear all,
> 
> I am tryng to compute the number of contacts between lipid molecules and 
>   protein during a simulation in order to get a semiquantitatve 
> information on time-dependent interactions between the two kinds of 
> molecuules, as suggested by Deol et al. in a recenty published paper 
> (Biophysical Journal, 87/6, 3737-3749).
> 
> I have used g_mindist command, but I have been only able to compute 
> contacts at atomic level between protein and lipid molecules 
> headgroups/tails: indeed, I would prefer to get a number that matches 
> the NUMBER of lipids in contact with the protein (e.g., 4 lipids --> 4 
> contacts). What do you suggest about it ? Should I use g_mindist or 
> anything else ?
How about surface area (g_sas)? You can even relate it (vaguely) to free
energy.
> 
> Thanks in advance
> 
> LM
> 
> 
> 
> 
> 
> 
> ..............................................................................................
> 
> Luca Mollica
> Dulbecco Telethon Institute (Biomolecular NMR Lab)
> 
> DIBIT-HSR,Via Olgettina 58, 1B4
> 20132 Milano (Italy)
> 
> Tel: 0039-02-26434824(Office)/26433497(Lab)
> Fax: 0039-02-26434153
> E-mail: mollica.luca#hsr.it
> 	luca_mollica#virgilio.it
> 
> "There is something to be learned from a rainstorm. When meeting
> with a sudden shower, you try not to get wet and run quickly along
> the road. By doing such things as passing under the eaves of houses
> one still gets wet. When you are resolved from the beginning,
> you will not be perplexed, though you will get the same soaking.
> This understanding extends to all things."
> 
> - Hagakure -
> 
> ..............................................................................................
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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