specific heat - instability

From: Alex Curutiu (alexcurutiu_at_gmail.com)
Date: Sun Aug 15 2010 - 05:49:52 CDT

Hi all,
I am having problems calculating specific heat, basically on each run (using
same configuration file and same positions/velocities ) I am getting a
different result. Finally I end up with testing from namd-tutorial files, to
be more precise with spec-heat example. I will present now the results I am
getting when I run namd ( 2.7b2 binary for linux and 2.7b3 for win32 ) for
ubq-nvt.conf from 2-5-spec-heat folder. The only change in the configuration
was the following line :"set inputname
./1-2-sphere/example-output/ubq_ws_eq" instead of "set inputname
./1-2-sphere/ubq_ws_eq ". Basically to point to the already computed
positions/velocities from tutorial files. A second change I made in the
configuration file is related to the number of steps, first I try with
100000, then I continue until 400000. I will present now the results I am
getting (I also try to increase the number of steps, but with no results):

linux

ID

Nr steps

( <E^2> - <E>^2)

 average.tcl script

Cv (J/(KgK))

1

100000

1309.54

3315.11

2

100000

2099.18

5314.07

3

200000

2686.75

6801.49

4

300000

3305.07

8366.78

5

300000

2416.38

6117.06

6

400000

3398.27

8602.71

7

400000

4058.48

10274.01

windows

ID

Nr steps

( <E^2> - <E>^2)

 average.tcl script

Cv (J/(KgK))

1

100000

2402.185

6081.12

2

100000

4265.493

10798.076

Would you please advise? Is there an instability in namd code? Should I run
more steps? What actually is the specific heat of Ubiquitin since I am
getting results from around 3000J/KgK until 10000 J/KgK. To duplicate the
problem is straightforward, as input I am using only data from tutorial of
namd,nothing else (configuration file from 2-5-spec-heat folder with the
change for original position/velocites to the one already computed (
basically to the onle present in the tutorial files) ). As executable I am
using as well form namd web site. I run the simulation on a single core /
single processor. Is there any chance to compute specific heat with namd or
Thank you very much.

-- 
Best Regards,
Alex Curutiu

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