[gmx-users] Constrain, ensemble.
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Mon Apr 29 21:25:58 CEST 2002
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
> 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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