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

Binbin Liu bmbbl at bmb.leeds.ac.uk
Wed Mar 2 12:21:18 CET 2005

Sorry I am confused by using tpbconv to make a new .tpr. 

What I have done is I run the command: tpbconv -s old.tpr -e old.edr -f 
old.trr  -o tpxout.tpr

The warning is "You've simulated long enough. Not writing tpr file".

Certainly I have a full range of simulation already. What I want really is a 
upgrade .tpr file so that I could use that to generate an ion.

Is there other ways to get a upgraded .tpr file?
> > 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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