(no subject)

LAMMPS LAMMPS Mailing List Mirror
1

Dear users,
I got a serious problem of doing nvt. My system contains ZnO and when I am doing nvt the temperature increases very much. The temperature increases from 300K to 300000K. But I know It should not increase. Please suggest me how can I overcome this problem.
My input script is below:

Generated with Gro2lam

units real
boundary p p p
atom_style full

atom_modify map array
pair_style lj/cut/coul/cut 8.5 10
bond_style hybrid gromos harmonic
angle_style hybrid cosine/squared harmonic
dihedral_style charmm

read_data /home/sasthi/Documents/gromacs_jobs3_F/zno+glu+water_F/zno-4-15-10/FINAL/g2l_dir/data.gro2lam

neighbor 1.9 bin
special_bonds lj/coul 0.0 0.0 0.0
pair_modify shift no tail yes mix geometric
neigh_modify every 1 delay 1 check yes

timestep 0.001
thermo 10
thermo_style custom step temp press vol epair emol etotal enthalpy

velocity all create 300 1234567 rot yes dist gaussian

fix nve_name1 all nve
run 1000
unfix nve_name1

fix nvt_name1 all nvt temp 300 300 10
thermo_modify lost ignore
run 1000
unfix nvt_name1

fix npt_name1 all npt temp 300 300 10 aniso 10 1 1000
run 1000
unfix npt_name1

dump 1 all xyz 10 file4.xyz
dump_modify 1 element NULL NULL NULL OE OW NULL NULL NULL NULL NULL &
NULL C NULL NULL NULL NULL NULL NULL NULL HC H NULL NULL NULL NULL NULL &
NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL &
NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL& NULL NULL NULL NULL NULL NULL H NULL NULL NULL NULL NULL C NULL NULL O Zn OZ

fix nvt_name1 all nvt temp 300 300 10
run 100000000
thermo 10
thermo_style custom step temp press vol epair emol etotal enthalpy

write_restart restart.g2l_400fs_new
Regards
Sasthi

2

Dear users,
I got a serious problem of doing nvt. My system contains ZnO and when I am doing nvt the temperature increases very much. The temperature increases from 300K to 300000K. But I know It should not increase. Please suggest me how can I overcome this problem.

this is usually an indication of bad force field parameters or a bad geometry.

axel.

3

Also your damping factor’s too high for temperatures in both NVT and NPT, and also for Pressure in NPT.
As per lammps manual, it must be around 100*(timestep) = 0.1, whereas in your case you have kept it 10, which is 10000*(timesteps). Same applies for iso argument in NPT.

4

Thank you Axel and Deep for the clarification. When I run the system in gromacs, its working fine. The temperature is constant or fluctuates a little bit. So I think my geometry should correct and I put same force field parameters that I put in gromacs. The simulation is working fine in gromacs and I got the results as expected. Is there any other reasons for failing the temperature constant in lammps?

Regards
Sasthi

5

please note, that gromacs uses different units than what LAMMPS has with “real”. it is easy to have typos there.

axel.

6

Did you consider changing your damping factors in your both fixes?

7

Dear DEEP,
I also changed the damping factor but the temperature is again increasing a lot. My modified input is below:

Generated with Gro2lam

units real
boundary p p p
atom_style full

atom_modify map array
pair_style lj/cut/coul/cut 8.5 10
bond_style hybrid gromos harmonic
angle_style hybrid cosine/squared harmonic
dihedral_style charmm

read_data data.gro2lam

neighbor 1.9 bin
special_bonds lj/coul 0.0 0.0 0.0
pair_modify shift no tail yes mix geometric
neigh_modify every 1 delay 1 check yes

timestep 0.001

thermo 10
thermo_style custom step temp press vol epair emol etotal enthalpy

velocity all create 300 1234567 rot yes dist gaussian

fix nvt_name1 all nvt temp 300 300 0.1
thermo_modify lost ignore
run 1000
unfix nvt_name1

fix npt_name1 all npt temp 300 300 0.1 aniso 10 1 1000
run 1000
unfix npt_name1

Any more suggestions?
Regards
Sasthi

8

Dear Sasthi

can you also share the data file?
I have noticed that the timestep you are using is 0.001 fs which is really very small. From my experience the usual timestep is around 1.0 fs for systems described by lennard jones interactions with partial charges. Why do you have to use such small timestep?

Also, is it possible to run simulations without using the “thermo_modify lost ignore” command? Do you get any error messages?

An alternative way of equilibration of your system is to use the nve/limit command (if there are overlaps you will get read of them by sufficiently long MD run). You can also try minimizing the energy before doing the NVT run (with the command minimize).

Regards
Evangelos

Στις Πέμ, 27 Ιουν 2019 στις 9:59 π.μ., ο/η Sasthi Charan Mandal <sasthi.phys@…43…4…> έγραψε: