[gmx-developers] GroupTrajectory Calculations

Mark Abraham Mark.Abraham at anu.edu.au
Sat Aug 6 03:15:36 CEST 2011

On 3/08/2011 11:59 PM, Mogo wrote:
> Hello to you all.
> In our research group we are developing several Potential Energy 
> Surfuces (PES) related with the Hydrogen combustion processes along 
> with trajectory calculations. We aim in the future to use these PES 
> and do calculations for a many particles system with different 
> species, allowing for the several reactions and channels to be 
> present, all at the same time. Meaning that one starts with a given 
> density for each of the different species involved and we let the 
> system evolve from this point on. In a long run a chemical equilibrium 
> should be reached.
> Having this in mind, I recently checked out Gromacs. It is a very 
> interesting programs which I think would be very useful for our project.
> It means to over the electrostatic equilibrium and let the several 
> atoms/molecules to react.
> Our trajectory calculations do exactly this but just for one 
> atom/molecule pair.
> I would like to know your opinion about the possibility of 
> implementing such processes in Gromacs, by making use of our 
> trajectory calculations routines, as opposed to building a new program 
> from scratch.
> What advices would you give?
> Do you have an idea if anyone tried something similar?

GROMACS and the classical MD forcefields it implements are built around 
the assumption that the chemical bonds present do not break and re-form. 
That's not necessarily a limitation for you, but you will need a 
functional form for pairwise interactions that can model both your 
bond-forming and non-bonding interactions at the appropriate distances. 
That might require the use of tabulated interactions, as described in 
the manual.


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