Calyff in Gromacs

Brief description of tools/files:
Iam new in Gromacs and

I am trying to use Clay.ff with Gromacs.

I added Clayff.ff directory in my working directory (downloaded from the link below: )

and I run the command:

gmx pdb2gmx -f xxx.pdb -o xxx.gro

I got the error message:

“Could not find any files ending on ‘.rtp’ in the force field directory”

Indeed the Clayff.ff directory did not have an rtp file.

What should I do?

Contact person (name and email address):
George Papamokos

How the work has been tested/reviewed:


I had a brief look at the files you link and this seems to be very initial work from “thomasunderwood” of porting the clay force-field to gromacs.

Trying to contact the author directly might help.

Here is a link to a publication where people used clayff and gromacs, they might be able to help you out:

I would echo the suggestion to contact the author, who has posted a tutorial but it lacks a lot of detail, starting from a pre-constructed topology. Note that this force field and its intended use is very different from “normal” GROMACS workflows and you cannot use pdb2gmx for it. Rather, topologies of surfaces and materials should be generated with x2top, which allows for the processing of generic species based solely on distances between the atoms.


I know I’m late to comment, but I use Clayff and Interface FF in Gromacs a lot. Let me know if you want any help…

Michael Holmboe
Umeå university, Sweden

Dear Michael Holmboe and Gromacs users,

We try to simulate nanocoposite comprising the substrate of aluminum oxide (Al2O3) and binder (different polymers (PS, PC, PMMC, etc.)). However, the CLAYFF force field has a limited number of bonded parameters to define the interactions for polymer binder. Is it possible to combine (without any significant problems) the CLAYFF force field with any other atomistic force field to simulate polymer-metal oxide composites in Gromacs?


It is doable to combine Clayff with other ff’s, but it has not really been designed for it. It is typically used with GAFF or OPLS as far as I know. As an alternative, the INTERFACE ff by Hendrik Heinz is supposed to be compatible with CHARMM/CGenFF, but overall it is likely very system dependent, and hence the best approach in mixing inorganic and organic ff’s is likely to try out a few different combinations of them, (like Clayff or Interface ff mixed with GAFF, OPLS, CGenFF), and then see how sensitive the results are to the choice of combination of ff’s.

What forcefield did you have in mind for the polymers? You can contact me directly if you need to see some examples of Clayff/Interface ff’s mixed with organic ff’s.


Michael Holmboe
Umeå university