Hi Amber Users,
I am calculating heat capacities at constant pressure for some ester
molecules.
My input file looks like this:
*trajin ../mdcrd_298matrix mwcovar name mxcvmat :650analyze matrix mxcvmat
thermo*
I get an out put that looks like this:
* ******************* -
Thermochemistry - ******************* temperature
298.150 kelvin pressure 1.00000 atm molecular mass (principal
isotopes) 296.47800 amu principal moments of inertia (nuclei only) in
amu-A**2: 718.47 8584.20 9048.46 rotational symmetry
number 1. Warning-- assumption of classical behavior for
rotation may cause significant error rotational temperatures
(kelvin) 0.03376 0.00283 0.00268 zero point vibrational
energy 1531620.7 (joules/mol) 365.82657
(kcal/mol) 0.5833521
(hartree/particle) Warning-- 66 vibrations have low frequencies and may
represent hindered internal rotations. The contributions printed
below assume that these really are vibrations.
freq. E Cv S cm**-1
kcal/mol cal/mol-kelvin
cal/mol-kelvin--------------------------------------------------------------------------------
Total
394.779 142.533 308.356*
I had a couple of questions regarding the output.
1. The output file refers the heat capacity at constant volume (Cv). So if
the trajectory analyzed was a NPT simulation, Is it safe to interpret this
value as the heat cap. at const. Pressure (Cp) ?
2. Is there anyway to specify the temperature at which the heat capacities
are evaluated? The output file states temp=298.15. Is there any way to
specify a different temperature if the simulations were conducted at that
temp?
3. Also, My simulation box has 650 molecules, and I noticed that the Cv
values are come out to be reasonable values only if I run this analysis for
1 of those molecules, else it returns NaNs. What might cause this?
Any help regarding this would be appreciated.
Thank you!
--
Vivek S. Bharadwaj
PhD Candidate
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
http://inside.mines.edu/~vbharadw/
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Received on Tue Apr 14 2015 - 15:00:02 PDT
