[gmx-users] distance and energy measure

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 7 13:20:54 CET 2002

On Mon, 7 Jan 2002, hugo verli wrote:

>Is there any command in gromacs to measure the average and/or variation 
>distance between two atoms in a molecular dynamics trajectory? And about the 

>interaction energy between a inhibitor and the enzyme? In this last case, is 
>there any way to measure the interaction energy between the ligand and each 
>aminoacid residue?
You can define energy groups (mdp file/ndx file) and then the interaction 
energy between all groups is stored in the energy file.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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