[gmx-users] Constrain, ensemble.

[Nguyen Hoang Phuong]

Dear David,

thank you very much. Now I would like to constrain all bonds of my
molecule except the bond C-N. It means I also have to edit the routine
make_shake? Thanks.

Phuong



> 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
> edit.
> 
> >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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