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

[Justin A. Lemkul]

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.

> 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?  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.

> The only way around was to rename the files in any of these manners:
> 
> 1) directory to gromos53a6b.ff and
> forcefield.itp therein to have include gromos53a6b.ff/ffnonbonded.itp 
> and gromos53a6b.ff/ffbonded.itp
> and point md.top to gromos53a6b.ff/forcefield.itp
> 

This should not be necessary.

> or
> 2) simply copy all files from ff directory to root and mention them in 
> md.top (forcefield.itp has to be changed afterwards)
> 

Copying all the files from the desired *.ff subdirectory into the working 
directory (of whatever name you choose) is a correct procedure.  There should be 
no need to manually modify the .top file, unless you're somehow manually 
generating it, as well.  With pdb2gmx, the modified files can be read like any 
other force field.

-Justin

> However both of these modifications are rather messy.
> -- 
> 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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