[gmx-users] dipole corrections to PME

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 22 13:26:36 CET 2002


For your information, I have tested the dipole corrections to PME in gmx 
3.1 (I admit I should have done this before release but anyway). The 
absolute fluctations in the total system dipole go down considerably, in 
particular when using small epsilon_surface. However you can compensate 
for that when computing the dielectric constant epsilon_0 (by an option to 

System: 820 SPC/E, cubic box, 2 ns, nstlist = 5, average and stddev over 
last 500 ps as measured with xmgrace
epsilon_surface	epsilon_0 (std.dev.)
1		84 (15)		==> vacuum boundary
30		74 (1.4)
78.5		65 (0.6)
200		71 (0.8)
inf		73 (0.9)	==> conducting boundary

Apart from eps_surf = 1, which is very noisy, the systems seem to behave 
well. It is a bit strange that at 78.5, the real dielectric constant, 
there is a minimum in the measured one, although the errors are larger 
than what's given here (the stddev of the running average, which 
basically says how well it converges).

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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