[MMTK] Hessian Matrix

santhu kumar mesanthu at gmail.com
Tue Jan 10 18:41:37 UTC 2012

Hello all,

I am new to MMTK and have looked around a bit to get to what I want.

I want to compute the Hessian matrix for given protein conformation using
force-field. Here are the steps I have done

#create universe
universe = InfiniteUniverse(Amber94ForceField())
#add protein to Universe
universe.protein = Protein(pdbFile)
energyAndHess = universe.energyAndForceConstants()
hess = energyAndHess[1].array
numAtom = hess.shape[0]
#reshape hess
hess.shape = numAtom*3,numAtom*3
#make it symmetric
he = numpy.triu(hess)
hess = he + he.T - np.diag(hess)*np.eye(hess.shape[0])

Am i correct in obtaining hessian this way?

I want to check my hessian matrix, just to make sure, with Gromacs. I was
able to generate the hessian but both the matrices do not match.
I see that it is possible that I am using a completely different set-up
than that is used in MMTK's universe. If I have to do that, what is the
configuration file I have to use for Gromacs? If not, is there anyway I can
check my hessian's validity?

Thanks a lot
Have a good day,
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