[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2
teemu.murtola at cbr.su.se
Fri Oct 22 15:37:11 CEST 2010
On Thu, Oct 21, 2010 at 14:28, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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.
This sounds wrong. The code in 4.5.1 always checks (or at least
should check) the directory of the including file first, and only if
the file is not found there, it continues the search in other
locations. Indeed, I did a simple test with gmxdump -p, and could not
reproduce this behavior; the file in a subdirectory of the current
directory was properly included also for the first syntax. Can you
make a simple test case that actually manifests such a behavior and
upload a bugzilla? Does it only occur with grompp, or also with
gmxdump -p (the latter does not support setting -I or -D, but should
otherwise behave identically)?
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