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

[Justin A. Lemkul]

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.berka at upol.cz <mailto:karel.berka at upol.cz>
> 
> ****************************************************************
> 

-- 
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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

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