[gmx-users] calculate number of contacts

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 1 20:06:58 CET 2006

On Wed, 1 Nov 2006, Attilio Vargiu wrote:

>Hi All
>I want to calculate the number of contacts between a small molecule and a
>oligonucleotide from a MD run.
>I read in the manual that in the itp file is possible, setting 2 for the
>combination rule within the section [ defaults ], to give sigma and
>epsilon instead of c6 and c12 LJ parameters.
>If I'm not wrong, the value of the interaction at the equilibrium point is
>-epsilon, so putting epsilon=1 for all but hydrogens atoms types in itp
>file, and setting a cutoff of 3.5 or 4 angstrom, re-running the trajectory
>with the proper groups in energy specifications, I should approximately
>get the number of contacts.
>Unfortunately this seems not to be the case, I get a number of contacts of
>one order of magnitude bigger than expected, but I do not understand
>what's going wrong...
>There is something I'm missing or misunderstanding?
>Can anyone help me?!?!?!?

you are mixiing things up. calculating the number of contact is done after 
a simulation using an analysis tool (g_mindist -on). This has nothing to 
do with simulation settings, topoogies etc.

>Thanks in advance
>Attilio Vittorio Vargiu
>PhD in Biophysics at SISSA/ISAS
>via Beirut 2-4, Trieste (Italy)
>phone: 00390403787335
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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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