[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Karel Berka karel.berka at upol.cz
Thu Oct 21 12:31:34 CEST 2010

> Karel Berka wrote:
> > Hi all,
> >
> > I have detected that preference in reading forcefield files in Gromacs
> > 4.5 has probably been changed from Gromacs 4.0.x and older.
> > In older gromacs, when there was forcefield with modification present in
> > my working directory, then it was read preferentially, but now it seems
> > that forcefield is primarily read from /share/top directory - Am I right?
> >
> The working directory is still searched first.

Unfortunately, it is not, otherwise ff in subdirectory of my working
directory would have been first one to use for grompp.
However, pdb2gmx was working fine for protein and ions around.

> In 4.5.2 I have tried to have modified gromos53a6.ff in my working
> > directory, but the modification was not used by gromacs.
> >
> What do you mean "not used"?  Was the wrong force field called when using
> pdb2gmx?

I did not used pdb2gmx since I am simulating membrane protein.
The only place when I needed to include forcefield itp was grompp program in
use on computer cluster , where I cannot reach /top directory

> Gromacs prints a list of force field subdirectories in the working
> directory, then in GMXLIB, and allows you to choose.  In the 4.5.x series,
> you
> need a full working subdirectory of the modified force field.
> FF.dat is not used anymore?


Zdraví skoro zdravý
Karel "Krápník" Berka

RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.berka at upol.cz

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