[gmx-users] To add all hydrogens

Xavier Periole x.periole at rug.nl
Mon May 22 18:05:03 CEST 2006

montserrat.vaque at urv.cat wrote:

> Dear All,
> First of all, I would like to give my thanks for the help David van 
> der Spoel has given us.
> I'm doing an energy minimization with mdrun without problems. However, 
> I've noticed that Gromacs is only adding the polar hydrogens and not 
> all the hydrogens during the energy minimization. I would like to know 
> if GROMACS is able to add all hydrogens and what I have to do, which 
> option I have to choose if it is possible.

Gromacs adds the hydrogen that the force field will us !!
You probably use the GROMOS force field which only use
explicit hydrogens when thesy are polar !!! If you want to
have all hydrogens described explicitely you have to choose
another force field when running pdb2gmx. OPLS is all
hydrogens ...


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

More information about the gromacs.org_gmx-users mailing list