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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 16 May 2018 18:36:13 -0400



On Wed, May 16, 2018 at 3:10 PM, Chuanxing Zhan <chuanxingzhan@...16...> wrote:
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?

​you've commented out fix shake. ​even a time step of 1fs is too large for that scenario. but cranking up the time step to 2fs explains the step in (average) energy.

axel.

 
#
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.

axel.

 
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... e.net> 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?

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.



--
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.