[gmx-developers] calculating poteintial energy into do_md()

Berk Hess hess at kth.se
Mon Jul 16 13:58:09 CEST 2012

On 7/16/12 13:05 , francesco oteri wrote:
> Dear gromacs developers,
> I am trying to implement in gromacs 4.5.5 a particular Hemiltonian 
> Replica Exchange tecnique.
> Right now, at every exchange attempt in do_md, I figured out  how to 
> access at the potential
> energy of replica A (=configuration A at temperature A) and B 
> (=configuration B at temperature B) and so on.
> In my case, each replica has the same temperature, but there is a 
> different Hemiltonian equation for every replica.
> The different Hemiltonian are obtained simply changing the force field 
> parameters in the input topology so I dont
> need to modify anything in gromacs.
> But at every exchange attempt I have to test if the configuration B 
> can exist in the state A so I need to calculate
> its potential energy using the force field data of replica A.
> I found that function sum_epot calculates the potential energy but I 
> suspect that it uses values calculated in
> do_force since sum_epot is called by do_force_lowlevel in turn called 
> by do_force.
> So my question is, should I call do_force in replica A with 
> coordinates from replica B reach my goal?
Are you changing bonded and/or non-bonded parameters?
Some non-bonded parameters might be preprocessed, so you might need 
reprocess those
and them reprocesses again to get back to the original state.

Note that 4.6 will have proper Hamiltonian replica exchange, but that 
will use the lambda coupling
parameter approach. If you need to do something similar, it might be 
much simpler to use this code.


> Thanks in advance,
> Francesco

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