[AMBER] No energy conservation in NVE ensemble amber 11

From: Ivan Gladich <ivan.gladich.marge.uochb.cas.cz>
Date: Thu, 24 Feb 2011 12:49:18 +0100

Dear Amber users
       I have a question about energy conservation in NVE simulation
using a Car-Parinello scheme (indmeth = 3) where in dipoles are assigned
a fictitious mass.
I have a cubic box of 1 Na+ and 1Cl- solvated in a 796 POL3 waters.
The system was
1)initially minimized
2)Using a Car-Parinello scheme to calculate the induced dipoles, I
equilibrated the system using periodic boundary condition with a
pressure coupling at 1 atm and a temperature of 300K for 1ns.
3)Finally, the final configuration of the previous step has been taken
as a starting point for 5 ns of a NVE simulation turning off the
thermostate (ntt=0). I performed two different simulation using two
different time step, 1 fms and 0.5 fms. I used Car-Parinello scheme
(indmeth = 3) for the calculation of the induced dipoles.

The strange thing is that the system does not conserve the energy. I am
a bit perplex because the energy shift is linear with time (90 Kcal/mol
in 5 ns!). The same trend is observable with the smaller time step.

I read some e-mail about energy conservation problem in previous amber
version; I am worried if the problem has been solved or if I made some
mistake in my parameter input list (attached).
Do you have any explanation of a possible reason for this linear shift
of the energy?
Thanks a lot
Ivan Gladich

Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
web page:http://www.molecular.cz/~gladich/

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Received on Thu Feb 24 2011 - 03:30:06 PST
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