[gmx-users] Question about creating new forcefield terms
gtg072j at mail.gatech.edu
Wed Oct 26 21:56:32 CEST 2005
I went through chapter 4 of the manual and there is no mention of the cubic
and quartic terms in the bond-stretch or bond-angle potential terms. So I
guess I have to incoporate that definition of the potential in the forcefield
file... Hence to do the Gibbsite simulations...
(1) At first, I have to define the potential energy equation somewhere. Can
you tell me where can I access the files that have the equations defined for
(2) Then I have to create *.itp, *bon.itp, *nb.itp, *.atp files (for which I
have the parameter data) and should also write up a small *.rtp file as well
(as Rahul mentioned)
(3) Incorporate the new ffxxx.itp in FF.dat so that I can use it to
generate .top and .gro files using pdb2gmx and go one from that point to
subsequently perform MD runs...
So I have to create all the files manually from scratch.....Is it the right
way to do MD on the system or am I making the situation very complicated?
Please suggest me accordingly if I am making a mistake in understanding the
Thanks a lot for your help,
Quoting David <spoel at xray.bmc.uu.se>:
> On Mon, 2005-10-24 at 17:19 -0400, Suchitra Konduri wrote:
> > Hi all,
> > I need a clarification on my simulation method. I am new to Gromacs and I
> > trying to do MD simulations on Gibbsite for which I want to use a modified
> > form of CFF91 forcefield that has cubic and quartic terms along with
> > terms. Since none of the forcefields in Gromacs i.e ffXXXXbon.itp have such
> > definition for both bond-stretch and bond-angle terms I assume that I
> > to create a new gibbsitebon.itp file and also create a new toplogy file to
> > include atom definitions. I have a pdb file for gibbsite from Material
> > and I tried using PRODG to obtain a .itp file but the atom types of the
> > Gibbsite structure are not defined in the database.
> You need to define the connectivity in the topology including the
> correct atom types. In the worst case you have to do it completely
> manually (chapter 5), but if you rename the atomtypes prodrg might help
> you. I think gromacs actually has the correct bonded terms, but check
> chapter 4.
> > Can someone please suggest me if there is a difefrent method of solving the
> > problem?
> > Thanks a lot for you help,
> > Suchitra
> > --
> > Suchitra Konduri
> > Graduate Student
> > Department of Chemical & Biomolecular Engineering
> > Georgia Institue of Technology
> > Tel: 404-894-8476.
> > _______________________________________________
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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Department of Chemical & Biomolecular Engineering
Georgia Institue of Technology
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