[gmx-users] How to obtain bond energy of the part of the system ?

David spoel at xray.bmc.uu.se
Sun Jan 18 14:50:01 CET 2004

On Sun, 2004-01-18 at 14:16, "?╔exТoi8-r?Q?" wrote:
> Hi Gromacs Community!
>   Suppose I have a system of a single hexane molecule in water and I run molecular dynamics for it. How can I obtain, for example, bond energy  of this hexane molecule only (not the whole system bond energy) or, say, kinetic energy of this hexane molecule (if I use thermostat for the whole system). 
>   Yes, we use energygrps tag in our input file but the appropriate edr file when processed with g_energy allows to get only coulomb and vdw interaction between the groups of our system. 
>   Thanks in advance, Alex.

if you use settle for water, the bond, angle etc. terms are only of your
hexane. Otherwise the bonded energies can not be split among groups.
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David van der Spoel, PhD, Assist. 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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