Amit Choubey wrote:
hi,
ok the next question that bugs me is if i make a directory consisting of
my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to
use pdb2gmx to get the *.top & .gro files according to the above new FF
files, how do i supply this info to pdb2gmx. In other words how do i
make pdb2gmx aware of the new FF files.
Make a new entry in (a local copy of) FF.dat.
-Justin
Amit
On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Amit Choubey wrote:
Hi,
so is it a good idea to edit the original gromacs files in top
directory for introducing new force field or is there a way to
compliment the existing FF files by a new file made by me?
It is generally better to not mess with system-level force field
files unless you're very sure of what you're doing, and experienced
in making such changes. If you alter one of the original force field
files, and you don't do it right, reverting the changes is often
difficult. If, for example, you want to modify the OPLS-AA force
field, do not ever make any changes to the original file, instead
implement them in files like ffoplsaa_mod.*
It is even safer to implement your changes in the local directory
until you are confident everything is working properly, then if
you're comfortable that you've done everything 100% right, move your
files into /share/top for convenience later.
-Justin
Amit
On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Amit Choubey wrote:
hi gromacs user,
Is there any good way to introduce new force field in the
gromacs library?
Read in the manual about the organization of existing force
fields,
as well as the component files that are necessary to make it
function. Beyond that, look at the implemented force fields
themselves and see how they work together.
-Justin
Amit
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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