[gmx-users] Constrain, ensemble.

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 29 21:59:58 CEST 2002

On Mon, 29 Apr 2002, Nguyen Hoang Phuong wrote:

>I would like to simulate a system with the following features:
>1) Unconstrain the bonds that involve H-atoms and constrain the rest bonds
This is the other way around... Usually one wants constraints on hydrogens
and not on heavy atoms. It will require some hacking in topshake.c if you
want to automate this. There is a routine make_shake that you need to

>2) NVE ensemble
If you turn off t and p coupling you have in principle constant energy. It
does require that you use PME (if you have charges), and a reasonably long
LJ cut-off. 

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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