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

From: Chuanxing Zhan <chuanxingzhan@...16...>
Date: Wed, 16 May 2018 19:10:04 +0000 (UTC)

Thanks for the current comment.
I did the test as Stefan said, ran the simulation at different time-step without restart command. For this test simulation, I remained all the parameter and setting ran short steps, but didn't allowed the  fix shake and fix imd commands. The simulation was only ran in npt ensemble at different time-step. And the figure clear show the energy jumped when time-step changed. 
The modified input script is posted here. And the new energy result figure was attached. Can you point out if there is anything wrong?
units           real
neighbor        2.5 bin
neigh_modify    delay 1 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 8 10
pair_modify     mix arithmetic
special_bonds   charmm
read_data       data.deca-ala-solv

#group peptide   id <= 103
#fix             rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23

thermo          100
thermo_style    custom step temp pe etotal press vol density
timestep        1.0
kspace_style    pppm 1e-5

fix             ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2

# IMD setup.
#fix  comm       peptide imd 5678 unwrap on trate 10

run 10000
timestep        2.0
run 10000

On Wednesday, 16 May 2018, 12:42:50 PM GMT-5, Axel Kohlmeyer <akohlmey@...24...> wrote:

On Wed, May 16, 2018 at 11:48 AM, Stefan Paquay <stefanpaquay@...24...> wrote:
This sounds like it might be specific to interactive MD simulations then, but I am not sure. Axel is more of an expert on that I think.

​but i cannot say anything, because the description being given is ambiguous. it is not clear what modifications were made to the example input, and whether the restarting was done correctly.​ in the vast majority of these cases, there is a mistake or misunderstanding in there somewhere, but without a crystal ball, it is impossible to detect and to give advice.


It just seems to me that it is weird that your energy should jump such a specific value upon a time step change.
Energy drift, however, is characterized by a very slow and gradual change of the total energy of the system, which is not at all what you are seeing.

On Tue, May 15, 2018 at 3:39 PM, Chuanxing Zhan <chuanxingzhan@...16...> wrote:
I ran a example in.deca-ala_imd under directory lammps-stable_11Aug2017/exampl es/USER/misc/imd.
I didn't change anything of example script except inserting restart command. I changed the time-step of system at 11000 step, then the energy jumped. I also checked the energy of the system, and is was continued in the whole simulation. Once I increase time-step, the energy  increase.
I just ran the simulation in one file without restart command. The energy of the system also increased when time-step increase. 

On Tuesday, 15 May 2018, 2:04:45 PM GMT-5, Stefan Paquay <stefanpaquay@...24...> wrote:

This most likely is not drift, because it looks like a sudden jump at a nicely round number of steps (10000). Which example did you run? Are all your pair styles and settings restart-compatible? If you do not restart but run twice as long, is the jump present or not?

On Tue, May 15, 2018 at 2:58 PM, Chuanxing Zhan via lammps-users <lammps-users@...42...> wrote:
Dear lammps users,
Sorry to send a wrong reply email before. I have questions about the energy drift of equilibrating system.
I ran a simulation and the equilibrated at different time-step. However, the energy results of same system show the different energy at different time-step. Then I ran a example script in the lammps example, the energy results of the example system  has the similar problem.

I know the "shadow" Hamiltonian may cause various energy results of same system at different time-step. Did the lammps compute the actual Hamiltonian mechanics of the system? Can anybody give any comments?


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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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