> > > 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.be...@upol.cz ****************************************************************
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