From: Axel Kohlmeyer (
Date: Tue Dec 24 2013 - 04:29:10 CST

On Tue, Dec 24, 2013 at 9:30 AM, Rasoul Nasiri <> wrote:
> Dear all,
> I have been trying to build up a tpr file in order to analysis my MD
> simulations by GROMACS.
> 1- My potential (ReaxFF) is not supported GROMCAS, therefore I have to
> construct tpr file manually, hopefully by VMD.

the topotools supports writing out a "fake" .top file that would allow
building a similarly fake .tpr file sufficient for most analysis tasks
in gromacs.

> 2- All bonds/charges are updated based on the bond order method.

> I just wondering whether there is any plug in in VMD can consider point of
> (2) for constructing a .tpr?

that would be utterly pointless, since the very basic assumption of a
.tpr file is that bonds and charges don't change (like VMD does, too).
with bond orders you don't really have a simple "is this is a bond?
yes/no" decision anyway. but rather you have a dynamic range.


> Best,
> Rasoul

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.