[gmx-users] Error in system_inflate.gro coordinates does not match

Justin Lemkul jalemkul at vt.edu
Fri Jul 11 23:19:57 CEST 2014

On 7/11/14, 2:57 AM, RINU KHATTRI wrote:
> hello gromacs users
> thank you justin i got system_shrink.gro after 20 energy minimization and
> shrinking next step is solvate your syetem but no command is there the
> command is there is
> grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
> -nname CL -nn 4
> which one is i have to use if both then i do not have system_solv.gro
> or system_solv_ions.gro (output)

Solvation is done with genbox.  See basic tutorials.  As stated in the membrane 
protein tutorial, it is assumed that you are comfortable with simple workflows 
and rudimentary commands.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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