Re: [AMBER] No energy conservation in NVE ensemble amber 11

From: Ivan Gladich <>
Date: Fri, 25 Feb 2011 11:50:23 +0100

Dear Mark,
            thank you for the link. Fixing dsum_tol =10^-6 and tol=10^-6
there is a sensible improvement of the results.
By the way there is still an energy shift of ~6Kcal/mol in 5 ns with a
time step of 1 fms.
The situation seems to get better reducing the time step (see attachments).

I am using a Car-Parinello scheme (indmeth = 3) for the calculations of
induced dipoles: I am wondering if it is this the problem.
In principle, this method should be faster than the iterative method
(indmeth = 1) but if I have to use a smaller time step, I do not now
know what is more convenient...


On 02/24/2011 12:37 PM, Mark Williamson wrote:
> Ivan Gladich wrote:
>> 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.
> Try increasing your SHAKE tolerance even further (tol=0.000001) and the
> direct sum tolerance:
> &ewald
> dsum_tol=0.000001,
> /
> This is quite a brief response, but for more details, have a read of
> this thread:
> Regards,
> Mark
> _______________________________________________
> AMBER mailing list

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:

AMBER mailing list

(image/jpeg attachment: graph_1.jpg)

(image/jpeg attachment: graph_2.jpg)

Received on Fri Feb 25 2011 - 02:30:05 PST
Custom Search