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From: Lekpa Duukori <duukori.gmail.com>

Date: Tue, 13 Jul 2010 12:16:54 -0600

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

Date: Tue, 13 Jul 2010 12:16:54 -0600

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:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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Received on Tue Jul 13 2010 - 11:30:03 PDT

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