[gmx-users] Counter-ion problem
spoel at xray.bmc.uu.se
Mon Jul 1 08:30:39 CEST 2002
On Mon, 2002-07-01 at 06:44, Jang Seokyoung wrote:
> Dear GROMACS USERS...
> I need your advice.
> I have -4.00 charge molecule and +1 charge molecule.
> I want to run normal M.D with this two Molecules in one system.
> but, I don't konw whether using Counter-ion or not.
> I think three cases.
> 1. using Counter ion ( 4 Na+ and 1 Cl- )
This or more ions, depending on the amount of water you have (compute
the concentration!). Combine with PME.
> 2. not using Counter ion ( Total charge -3.00 )
This you can only do if you think you can get away with using a cut-off.
> 3. Adding Hydrogen atom ( to make -OH instead of O-1 , and NH2 instead of NH+1 )
OH means low pH, NH2 iso NH3+ means high pH, so that is not
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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