Hello,
I am still having some trouble with the matrix
I am trying to get entropy estimates using the Schlitter formular (Chem Phys
Lett, 1993,215,617). I first do an rms fit to the first frame of my data
using the following ptraj commands ( I am using AmberTools 1.2)
trajin model.mdcrd.nowaters
trajout model.mdcrd.fit.nomass
rms first out rms.out.fit.nomass name rms
Then do
trajin model.mdcrd.fit.nomass
matrix mwcovar name mwcovar.name out mwcovar.out
I then use the following python script to calculate the entropy
#!/usr/bin/python
import numpy
sigma = numpy.loadtxt('mwcovar.out')
hbar = 1.054571628e-34 #Joules seconds
T = 300.0 # Kelvin
Kb = 1.3806504e-23 #Joules/Kelvin
Euler = numpy.exp(1)
constant = 10e-23 #Angstroms squared multiplied by g --> Kg (10^-3)
unit_matrix = numpy.eye(len(sigma[0]),len(sigma[0]),dtype=float)
matrix = (unit_matrix) + ((Kb*T*Euler*Euler)/(hbar*hbar))*sigma*constant
Entropy = 0.5*Kb*numpy.log(numpy.linalg.det(matrix))
But I get an infinite determinant and a NaN entropy, the elements matrix are
very large (10 to 26 or so)
I have done some dimensional analysis and think my units should be ok, but
the values in the matrix indicates otherwise so I don't know exactly what is
going wrong here. Any comments welcome.
Thanks.
Lekpa
On Tue, Jul 13, 2010 at 9:27 AM, Lekpa Duukori <duukori.gmail.com> wrote:
> Thanks Jason.
>
> Lekpa.
>
>
> On Mon, Jul 12, 2010 at 8:56 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Hello,
>>
>> Looking at rdparm.c, it appears as though the masses are read straight
>> from
>> the topology file without any modification (since I don't see it
>> multiplied
>> by any constant). The masses in the prmtop files are in atomic mass units
>> or g/mol. This is easy enough to verify, just by looking at the MASS
>> section of a prmtop file. You'll see lots of 1.401000E+01 (Nitrogen) and
>> 1.201000E+01 (Carbon) and 1.008000E+00 (Hydrogen).
>>
>> Hope this helps,
>> Jason
>>
>> On Mon, Jul 12, 2010 at 9:34 PM, Lekpa Duukori <duukori.gmail.com> wrote:
>>
>> > Hi All,
>> >
>> > Please does anyone know the units for masses used in computing the mass
>> > weighted covariance matrix in Ptraj?
>> >
>> > Thanks.
>> >
>> > Lekpa
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Jul 13 2010 - 11:30:03 PDT
