[gmx-users] solvent out of box with genbox

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Feb 12 16:24:24 CET 2006

Hi ALpay,

For computational reasons, gromacs usually uses the rectangular box
corresponding to the (probably more complex) shape you are using. This is no
problem, since it is always possible to convert a system in one box type
into any other box type, available under pbc. The configuration of the
infinite simulation system is not changed.


On 2/12/06, Nuri A Temiz <temiz+ at pitt.edu> wrote:
> Hello gmx users
> >
> >I am trying to simulate a Zinc-finger domain. I have searched the mailing
> list
> >about Zn-ligand interactions and i decided to fix the Zn since i am only
> >interested in keeping the fold stable.
> >But when i use pdb2gmx, the program automatically protonates the Cys S
> and
> His
> >NE2. I have checked the manual and fixed the His protonation states, but
> >could not change the Cys residues. In the manual, the section for Pdb2gmx
> >says that the program can be prompted to change Cys residueprotonation
> state,
> >but i did not see the option to do it.
> >I must also add that i just started to use Gromacs, so i may be missing
> >something.
> I have sent this email yesterday. I have already tried -cys on pdb2gmx
> which
> actually is not an option. Then i changed my cysteines by hand on topology
> file and added constraints on 2 cysteines,2 histidines and  Zn, also
> renumbered the topology and gro files.
> But everytime  i use editconf and genbox, most of my solvent is out od the
> box. I checked the box visually, the solute (zn-finger peptide) is in the
> center but about 3/4 of the solvent is out of the box.
> here are the commands i used for editconf and genbox''
> editconf -f speptide -o -bt dodecahedron -d 1.5
> genbox -cp out -cs -p speptide -o b4em
> by the way, i use gromacs 3.2.1
> any help would be great
> in the md it should not be a problem since i use pbc.
> but why do i see the shift in the solvent molecules visually when i use
> either
> vmd or ngmx.
> Thank you very much.
> ALpay
> --
> N. Alpay Temiz
> Department of Computational Biology &
> Department of Molecular Genetics and Biochemistry
> School of Medicine, University of Pittsburgh
> e-mail:temiz at pitt.edu
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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