[gmx-users] Adding ion to equilibrated system using genion...

David spoel at xray.bmc.uu.se
Tue Mar 1 21:10:21 CET 2005

On Tue, 2005-03-01 at 18:37 +0000, Binbin Liu wrote:
> Dear all,
> I ran hundreds of ps equilibrium simulation on the system with the input file: 
> 'eqb.tpr' and the equilibrated configuration output from mdrun is 'eqb.gro'
> Now I want to add an ion to 'eqb.gro' using genion. Certainly 'eqb.gro' 
> couldnt be taken as the input to genion. The only input for genion is 
> 'eqb.tpr' file. 
> My question is that because eqb.tpr only contains the configuration before the 
> equilibrium, is it really correct that applying this file to generate an 
> ion ?
make a new tpr using tpbconv.

> Thank you
> Best,
> Binbin 
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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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