[gmx-developers] energy calculation

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 14 12:57:54 CET 2002

On Wed, 13 Mar 2002, Erik Lindahl wrote:

>If you just want to know the energy of a structure based on a PDB file 
>it's probably much smarter to just use the normal gromacs programs, read 
>the file and perform '0' steps of any calculation. Since we're not 
>updating the coordinates ( 0 steps) you will get the energy of the 
>current structure. Usually this isn't very meaningful, since the 
>structure was derived with a different forcefield, and you would need to 
>perform at least an energy minimization to get a reasonable energy, but 
>that all depends on what you want to do...

If you want to do more involved things, it may be easier to modify mdrun 
directly. This will give you access to enighboursearching, PME etc.
Just modifying the contents of md.c will do, there the do_force routine is 
called with correct arguments that are initializated correctly.

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

More information about the gromacs.org_gmx-developers mailing list