[gmx-users] angular momentum.
spoel at xray.bmc.uu.se
Tue Oct 1 00:26:16 CEST 2002
On Mon, 2002-09-30 at 23:29, Nguyen Hoang Phuong wrote:
the simulations run with:
> rlist = 1.
> rcoulonb =1.
> rvdw = 1.
> PME was used.
> I wonder if these values cause the problem? After 10ps, the magnitude of
> the angular momentum is increased by a factor of 5, the timestep is
> 0.5fs and double precision is switched on. Within this short
> simulation time, does the numerical error of intergrations is big enough?
Could it be that your peptide is trying to align its dipole with it's
periodic images? Check the total system dipole as a function of time, or
redo the simulation with a larger box.
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