[gmx-users] residue index

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 11 14:47:41 CET 2008

tangxuan wrote:
> hi all,
> I want to calculate the contact in a index group by g_mdmat. However, 
> the residue index is not continuous in it because this index group is a 
> combination of two subunits(subunit1: residue 1-470, subunit2: residue 
> 2000-2470). When I use g_mdmat, a very huge matrix is  produced and a 
> lot memory is needed. It is very slow to do this calculation. Does 
> anyone know how to solve this problem? Is there a way to make residue 
> index continuous?
Now I understand the problem. I'll fix it.

> Tang
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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