[gmx-users] force-field parameters
spoel at xray.bmc.uu.se
Fri Aug 30 21:26:25 CEST 2002
On Fri, 2002-08-30 at 21:14, David L. Bostick wrote:
> You can rename the file to something that doesn't exist in the distributed
> /top directory and in the top of you mdp file specify..
> include = -I$GMXDATA/top -I./
> although the -I./ is probably unnecessarry because I believe the current
> directory is already searched when grompp puts together the topology. If
> you really want to be sure you use nothing in the /top directory, just dont
> include it with -I$GMXDATA/top. I think this is right although please
> somebody correct me if not.
The working directory is always searched first. Furthermore you can
check the topology using gmxdump. Look for idef, and you'll find the
matrix of LJ parameters written out linearly (i.e. row1, row2, .. rowN)
so for 20 different atom types you will find 400 LJ parameters.
> David Bostick Office: 262 Venable Hall
> Dept. of Physics and Astronomy Phone: (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall dbostick at physics.unc.edu
> Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> On Fri, 30 Aug 2002, Rui Qiao wrote:
> > Hi list:
> > I am trying to study the influence of forcefield parameter on the
> > simualtion results. In doing that, I change the forcefield parameters in
> > the .itp file and I have put them in my working directory.
> > My concern is that will Gromacs try to use the parameters in my
> > working directory or it will try to use the original "itp" file Gromacs
> > has (in some directory like .../share/top/)?
> > Thanks a lot for your time.
> > sincerely,
> > Rui
> > ------------------------
> > Rui Qiao
> > Research Assistant
> > Beckman Institute, UIUC
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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