[gmx-users] Re: Charge groups II

David van der Spoel spoel at xray.bmc.uu.se
Sat May 18 10:34:58 CEST 2002

On Fri, 17 May 2002, Pedro Alexandre de Araujo Gomes Lapido Loureiro wrote:

>> By the way, which gromacs version was this?
>>Can you send me a .tar.gz file?
>I would have to send you my modified force field also (I am using the GROMOS 96
>45a3 forcefield for lipids). This would give you a lot of boring work...
>I am convinced that the problem arises from the single charge group (in the
>headgroup) and/or the partial charges of Chiu, as you suggested.
>If I use lower partial charges and/or smaller charge groups (those in the .itp
>file I have sent) the problem seems to disappear.
Tieleman & Berendsen have done a comparison of force fields for DPPC, and
concluded that those half-charges are not necessary, and they had some
more recommendations as well. (D.P. Tieleman and H.J.C. Berendsen,
Molecular dynamics simulations of a fully hydrated
dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary
conditions and parameters, J. Chem. Phys. 105 (1996) 4871-4880.)

Maybe you should have a look at that. 

Another detail that you could try is the LJ, try without the shift
function, plain twin range cut-off at 1.0/1.6 or something like that.

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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