[gmx-users] setting cut-off for coulomb interaction
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 29 08:37:19 CET 2001
On Wed, 28 Nov 2001, Rui Qiao wrote:
> I used cut-off for coulomb interaction in my simulation, and when
>I am using:
> rcoulomb = 2.4 (my simulation box is 5nm), the energy minimization
>give lowest potential energy to be -7.8e4, however, if I change
> rcoulomb = 0.9, it give a number of -1.15e5.
> Actually I am expecting it to be around -1.5e5 becuase I am having
>3600 water moleculars (using PME to do the simulation yields a number
>around -1.1e5 too). What confuse me is why when using a larger cutoff
>radii give a "bad" result.
Energy minimization will not do this for you, only local contacts will be
adjusted. If you run dynamics however, the energy will go down to roughly
-42 kJ/mol for pure water.
> Another question is that when using plain cutoff, shall I specify
>the epsion_r for water? The example problems online seems does not give
>such an epsion_r.
epsilon_r should be 1, otherwise your system will blow up. If you e.g. set
epsilon_r to 2, you effectively half the Coulomb forces without modifying
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-users