[gmx-users] charge on protein

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 23 17:32:30 CET 2005

On Sun, 2005-01-23 at 21:29 +0530, 4tejender wrote:
> hello users
>  i m new to gromacs can anyone tell me it is advisable to simulate protein with high charge.does it effect reliablity of the dyanamics. if yes what is a proper method to reduce the charge. i m getting waring for a non zero charge of -15.000e during processing protein file.

that is quite a lot. If you don't add ions it may even unfold due to the
charge. Be careful with a long equilibration of the solvent and ions
(e.g. run 2-5 ns with position restraints on the protein).
> thanks in advance
> teje
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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