[gmx-users] Hydrogens in lipid bilayer

Andreas Kukol A.Kukol at warwick.ac.uk
Fri Jul 22 16:09:02 CEST 2005

These are united-atom forcefields. Most hydrogens, apart from polar hydrogens, are not represented explicitly. For all hydrogens use OPLS.


>>> nagaraju_cy at yahoo.co.in 22/07/2005 13:13:01 >>>
Dear gmx-users,
                I am new user to gromacs. I used
GROMOS96 43a1, GROMOS96 43b1, GROMOS96 43a2 force
field by pdb2gmx command, none of these force field
added all hydrogens to the protein. 

In this site to the lipid bilayer hydrogen atoms are
not present in pdb files as well as in dppc.itp,
lipid.itp files. 
        Does gromacs consider hydrogen atoms in
dynamics calculations. If it consider in calculations
how to get topology files that contains hydrogens.
PRODRG2 server   gives gromacs topology file only for
heavy atoms, how can i get hydrogen containing
topology files.  
     Thank you 

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