Karel Berka wrote:
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.
My guess is that this is a matter of how the force field was #included in the
.top file. For instance:
#include "my.ff/forcefield.itp"
will match $GMXLIB first, but
#include "./my.ff/forcefield.itp"
will match the working directory first. Is this perhaps the issue you're
finding? Other simple #include statements (like #include "ions.itp", etc) still
use the old order of preference, but subdirectories make that a bit more difficult.
> 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?
No. The list of force fields is populated from the *.ff entries in the working
directory and $GMXLIB.
-Justin
-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 <mailto:karel.be...@upol.cz>
****************************************************************
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
