[gmx-users] where is water?

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 11 18:38:26 CEST 2011

Ragothaman Yennamalli wrote:
> Hi Friends,
> When I run pdb2gmx, it automatically asks which water topology should be 
> included. Also, in the .top file the lines included are:
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
> However, I do not see any water molecules in the .gro file. So, was 
> water included or not?

pdb2gmx does not add water.  That's what genbox does.  The water selection 
utility in pdb2gmx is intended to make your life easier when it comes to 
solvation - the water topology is already present (#included in the .top).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list