[gmx-users] Question about creating new forcefield terms

David spoel at xray.bmc.uu.se
Mon Oct 24 23:53:18 CEST 2005

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 am
> 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 quadratic
> terms. Since none of the forcefields in Gromacs i.e ffXXXXbon.itp have such as
> definition for both bond-stretch and bond-angle terms  I assume  that I have
> 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 Studio
> 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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