[gmx-users] charged proteins

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 8 14:34:30 CET 2002

On Fri, 8 Mar 2002, Berk Hess wrote:

>I would say for any system with water, including a charged or
>uncharged protein and some or no counterions use at least a
>reaction field. Even in pure water a plain cut-off will give
>terrible artifacts.
>PME is more accurate than reaction-field, but not much,
>especially in a high dielectric solvent like water. You will
>have to choose for yourself if the gain in accuracy is worth
>the performance penalty. Also for very small systems PME might
>give periodicity artifacts.

Didn't you suggest using a 1.5 nm cut-off with RF? When used as a single 
cut-off that will be much slower than PME with a cut-off of 1.0.
When used as twin-range, you introduce other artefacts, including worse 
energy conservation. As we've shown in the GROMACS 3.0 article an 
acceptable cut-off scheme (0.9/1.4) is not much slower than PME, but still 
considerably less accurate.

It's high time someone tests these things systemetically, and publishes 

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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