[gmx-users] computing contacts

[Luca Mollica]

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 ?

Thanks in advance

LM






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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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