Hi,
First, note that this really is a more advanced kind of analysis and
you need to take care with how you perform it. In particular you need
to make sure you are using a mass-weighted covariance matrix, and that
it is determined from many more frames than the number of coordinates
(i.e. # atoms * 3). Also I believe that the 'thermo' analysis assumes
no prior fitting (i.e. the molecule is diffusing/rotating freely), so
the first mode considered is the 7th one. In general it's a good idea
to post your entire input and describe exactly what you're doing with
your calculations.
On Tue, Apr 14, 2015 at 3:42 PM, Vivek Shankar Bharadwaj
<vbharadw.mymail.mines.edu> wrote:
> 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) ?
Since the statistical mechanical formulas used by 'thermo' are really
for an ideal gas in the canonical ensemble, technically no. However, I
think that if the system is relatively large and as long as you're not
near a phase transition the two ensembles are mostly equivalent
anyway.
> 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?
Not with ptraj. You can do it with cpptraj however.
> 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?
The covariance matrix for 650 molecules is much larger than it is for
1, so you need more data. My feeling is you may not have enough frames
to properly populate the matrix, which should be much greater than
'650 * # atoms per molecule * 3 coords per atom'. However I think that
since the equations are for internal vibrations they aren't really
valid for more than one molecule anyway (others may want to correct me
if I'm wrong here).
Hope this helps,
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 21 2015 - 11:30:02 PDT
