[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:

>Hi, there:
>	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
the LJ.

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

More information about the gromacs.org_gmx-users mailing list