From: Axel Kohlmeyer (
Date: Tue Dec 24 2013 - 12:04:09 CST

On Tue, Dec 24, 2013 at 6:42 PM, Rasoul Nasiri <> wrote:


> Sorry, I was assuming that analyses are under consideration which can be
> influenced by charges and chemical bonds since those are being collected in
> *.tpr.

did you see this anywhere in the documentation? making such
assumptions without any corroborating evidence is extremely dangerous

> If charges and bonds are considered as fixed values in .tpr, how one can
> perform the analysis properly?

does gromacs support reaxff? no! so why does it matter to the gromacs

> Having said this, is there any way one considers flexible
> values for those in .tpr file?

how should they get in there? and why should this be done with
analysis tools for a simulation package that doesn't have a need for

> For an example, I'm interest to know how much chemical bonds affect dynamic
> behavior of molecules in interface (liquid-gas) and finally on heat and mass
> transfers on fuel droplets in nano-scale.

this statement is for the most part just buzzwords without any
specific meaning. to give them meaning you have to figure out which
specific indicators can be used to draw conclusions from your
simulations. as i stated before, these kind of considerations
typically have to be done when planning your simulations. running the
simulations itself is usually the simplest task. and for something as
unusual as reaxff, you have to be prepared to write your own analysis
tools. or search if there are analysis tools or at the very least
preprocessing tools to be used for the simulation package you use.

this is now getting extremely off-topic for a mailing list on VMD, so
lets close this topic.


> Best,
> Rasoul

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