[gmx-users] problem regarding pbc

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 24 09:45:02 CET 2007

Hi Sangeeta,

To start with, you don't really describe a problem regarding pbc, as
you've stated in the subject. Please make the subject reflect your
problem or question directly. This will make it easier on the repliers
on this list to check whether they can be of any help. Most of us
read/discard messages based on the subject.

Now, you have three questions, which you've stated before, but
apparently the answers were not informative enough. To start with the
pbc, gromacs uses pbc unless explicitly stated otherwise, by adding
pbc=no in the .mdp file.

Regarding the chlorides, I think you caught that you have to have an
#include statement in the .top file, reading #include "ions.itp". The
next thing to make sure is that the name you've used for your chloride
ions in the .top file matches those in the file ions.itp listed for
the force field you are using. It may be CL, Cl, Cl-. You can try
either or you can check the file ions.itp in your
$GMXDIR/share/gromacs/top directory.

Finally, regarding dssp, please explain what you tried to do, i.e.
which command you've issued. Note that the file you mentioned is
merely a temporary file.

Hope it helps,


On 1/24/07, sangeeta <sangeeta at bic.boseinst.ernet.in> wrote:
> Dear GROMACS list members,
>    I have three questions,
>    My protein has +2 charge, so I added two Cl atoms through the program
> genion and subsequently edited the  topol.top file, in spite of that while
> running mdrun it gave an error that  "FATAL error, CL atom type can not be
> found",I can not understand the problem.
>    I wanted to include PBC in my simulation, I want to know that does
> Gromacs by default use the option by minimum image convention or we have to
> edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is
> being included in my simulation?
>     In spite of having dssp and running it I can not get the .xpm files.
> Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx
> are being produced.How can I generate those xpm files?
>     Waiting for your reply.
> regards
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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