[gmx-users] Where are equilibrium values stored?

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 4 09:52:38 CEST 2004

On Tue, 3 Aug 2004 j.m.shy+csuohio.edu at sims.csuohio.edu wrote:

>Hello everyone,
>I'm writing a program to work with Gromacs and, since I'm a relatively new user, perhaps someone can 
>tell me what variables equilibrium bond angles, bond lengths, and equilibrium dihedral angles are 
>stored in. 
Check topology->idef.iparams
(data structures in include/types/idef.h)
>Also, am I correct to assume that these values, once they are read in (from, for example, a .tpr file), are 
>modified during an optimization such as that performed by do_lbfgs? If so, where exactly (in do_lbfgs)?
The references are not modified by the program, only the coordinates.
>Any and all help is much appreciated.
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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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