[gmx-users] steady

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 7 15:51:09 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> I made a file with  (n1/n2=30) two solvents.I want to equilbrate this
> file.then I must minimize and run md(pre md ).please correct me if It
> is not right.
> I use
> editconf   -f test42.pdb(this file)    -bt dodecahedron     - d 0.5 -o box.gro
> as you tell for delet periodicity
> editconf   -f  box.pdb    -princ  -pbc   -vdwread
>  I could  minimiz it.and now  I have  a distorted file .how can steady
>  and smooth .

What do you mean distorted?  The default output will be rendered such that it is 
in a triclinic box, which can be corrected with trjconv -ur compact -pbc mol.  I 
have never found editconf -pbc to be entirely reliable.


> do you think I have to do long md for it or another else?
> best and thank you


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list