simulation box size and volume

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1



Hi all.







I am study about interacition between protein and water.







I have simulated about ten cases.







I put specific simulation box size unsing command. ( 24 * 24 * 24 )







Firstily I used NPT ensemble.







But box size was expanding during simulation time.







(I saw taht in VMD)







So I changed model using NVT ensemble.







But it still expnaded.







I checked log files and then found out temp, press, and volume were kept constant.







Here are my questions.



1. Is there any differences between simulation box and volume that is in thermo output?



2. How to fix simulation box size during simulation time?







I always appreciate your work.







Sincerely.







- Hongmin











* I attached my input file







1. for relaxation



---------------------------------------------------------------------------------



# Created by charmm2lammps v1.8.1 on Mon Apr 11 01:43:14 KST 2011



units real
neigh_modify delay 2 every 1
boundary p p p



atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic



pair_style lj/charmm/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-4



read_data B_13.data



special_bonds charmm
fix 1 all shake 1e-6 500 0 m 1.0 a 23
fix 2 all npt temp 300.0 300.0 100.0 iso 0.9869 0.9869 500.0
neigh_modify page 1000000 one 20000



thermo 10
thermo_style multi
timestep 0.05



restart 10 B_13.restart1 B_13.restart2
dump 1 all atom 50 B_13_relx.dump
dump_modify 1 image yes scale yes



run 1000000



--------------------------------------------------------------------------------







2. for trajectory(NPT)



--------------------------------------------------------------------------------



# Created by charmm2lammps v1.8.1 on Tue Apr 12 01:08:37 KST 2011



read_restart B_13.restart2




group H14 id 41 13 14 15
group H15 id 42 15 14 13




kspace_style pppm 1e-4
fix 1 all shake 1e-6 500 0 m 1.0 a 23
fix 2 all npt temp 300.0 300.0 100.0 iso 0.9869 0.9869 500.0
neigh_modify page 10000000 one 20000



compute 1 H14 dihedral/local phi
compute 2 H15 dihedral/local phi



thermo 10
thermo_style multi
timestep 2



dump 1 all atom 10 B_13.dump
dump 2 H14 local 5 dihedral.H14 c_1
dump 3 H15 local 5 dihedral.H15 c_2



dump_modify 1 image yes scale yes



run 225000
--------------------------------------------------------------------------------




3. for trajectory(NVT)



--------------------------------------------------------------------------------



# Created by charmm2lammps v1.8.1 on Tue Apr 12 01:08:37 KST 2011



read_restart B_14.restart2




group H11 id 38 10 9 8
group H10 id 37 8 9 10




kspace_style pppm 1e-4
fix 1 all shake 1e-6 500 0 m 1.0 a 23
fix 2 all nvt temp 300.0 300.0 100.0
neigh_modify page 10000000 one 20000



compute 1 H11 dihedral/local phi
compute 2 H10 dihedral/local phi



thermo 10
thermo_style multi
timestep 2



dump 1 all atom 10 B_14.dump
dump 2 H11 local 5 dihedral.H11 c_1
dump 3 H10 local 5 dihedral.H10 c_2



dump_modify 1 image yes scale yes



run 225000
---------------------------------------------------------------------------------

2

Hi Hongmin,

If you use NPT, shouldn’t that change Volume (V=L^3) and hence L (box size) with changes in pressure §?. If your box size is changing in NVT, then you must have been using “fix deform” or “displace box” command, otherwise it shouldn’t !! “fix deform” or “displace box” is used to modify box size during simulation (check the manual).

Monojoy

3

Hi all.
I am study about interacition between protein and water.
I have simulated about ten cases.
I put specific simulation box size unsing command. ( 24 * 24 * 24 )
Firstily I used NPT ensemble.
But box size was expanding during simulation time.
(I saw taht in VMD)

how did you determine that? are you sure that you
didn't see just the diffusion of water molecules?
coordinates are automatically unwrapped when loading
standard lammps dump files into VMD. you'll have
to use the pbc wrap command from the pbctools plugin
if you want coordinates to be wrapped back into the
principal simulation cell.

So I changed model using NVT ensemble.

so you probably wasted a lot of time. :wink:

But it still expnaded.

the simulation cell, _cannot_ expand in nvt ensemble.

I checked log files and then found out temp, press, and volume were kept constant.

of course.

Here are my questions.

1. Is there any differences between simulation box and volume that is in thermo output?

no.

2. How to fix simulation box size during simulation time?

there is nothing to fix but your perception. :wink:

cheers,
    axel.