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Re: [lammps-users] Energy rise
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Re: [lammps-users] Energy rise


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 4 May 2018 16:14:03 -0400

On Fri, May 4, 2018 at 12:54 PM, Chuanxing Zhan via lammps-users
<lammps-users@lists.sourceforge.net> wrote:
> Thanks for your advice. I did the test. The energy doesn't change if I keep
> the same time step, it will rise if I increase the time step. I also agree
> with your point, the energy result should not relate to time step. I don't
> think I changed any other parameter in my scripts.

it is difficult to give any more specific advice without actually
having a simple test case.
are you certain, that your system is able to run an MD in a stable
fashion at a 2fs timestep?
in other words, does your system, when run without a thermostat,
conserve energy?

you mentioned, that you are looking at small organic compounds. for
those often 0.5fs or less is required unless you use constraints on
all bonds to hydrogen atoms.
the graph you produced would be consistent with a scenario where you
do not have constraints, and then your thermostat compensates for the
instability. in that case, your average temperature would be above the
desired target.

axel.


>
> Kerwin
>
>
> On Friday, 4 May 2018, 11:32:10 AM GMT-5, Valerio Sorichetti
> <valeriosorichetti@...24...> wrote:
>
>
> Dear Kerwin,
>
> I would say that changing the timestep shouldn't give that result, but why
> don't you test it yourself?
> Try to do the same without changing the timestep and see whether the problem
> persists.
>
> Valerio
>
> 2018-05-04 18:14 GMT+02:00 Chuanxing Zhan <chuanxingzhan@...16...>:
>
> It did happen at restart process. And the only change is time step. When I
> turned  the time step form 1fs to 2fs, the energy of system rose.  Is that
> the problem?
> On Thursday, 3 May 2018, 5:42:49 PM GMT-5, Valerio Sorichetti
> <valeriosorichetti@...24...> wrote:
>
>
> Dear Kerwin,
>
> Does this happen as soon as you restart the simulation?
> If this is the case, such a sudden increase in the energy could come from a
> change in the the mass of a group of atoms, or in the parameters of the some
> interaction potential (or in those of a bond type).
> Check that you are not changing anything important when restarting the
> simulation.
>
> Valerio
>
> 2018-05-04 0:09 GMT+02:00 Chuanxing Zhan via lammps-users
> <lammps-users@...396... sourceforge.net>:
>
> Dear Lammps Users,
>
> Hello, everyone. I used the lammps to equilibrium small organic system. The
> system seems equilibrated after a long simulation period under npt ensemble.
> However, when I continued to run the simulation, the energy increase at a
> point and enter to equilibration again. Dose anyone know what happen with
> the system, or is this result reliable? Any help would be appreciated.
>
> Kerwin
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.