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

[Karel Berka]

>
>
> 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?

-Justin
>


-- 
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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