[gmx-users] charged proteins

[David van der Spoel]

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 
it.

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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