Dear all
I have changed the potential from Charm to cut/cool/long . Even then there is large fluctuation in pressure.I had gone through all the parameters i have used again and again. But couldn’t locate any error.Now i am attaching my input file. Please help me to get a solution for this.
Thanks in advance
Jesseela
in.waterNPT5 (2.09 KB)
Jesseela:
If you are seeing the instantaneous pressure change in the range of hundreds of atmospheres, that’s actually fairly typical of MD simulations. So long as the long-term average is correct, and the fluctuations are decreasing with time (constant magnitude, divided by increasingly larger number of samples), I don’t think there’s actually a problem that can be fixed.
–AEI
Hi
Thank you for your suggestion.In my case the fluctuations are not decreasing with respect to time. I have calculated the long time average (average of 1000 time step) of pressure . That is also found to be fluctuating. Also i have tried by changing the time step from 1fs to 2fs. No change in fluctuation happens even after 10 million time step.
jesseela
#Input file for SPC/E water
boundary p p p
restart 50000 restart
#Simulation Units andSimulation Type
units metal
atom_style full
#Reads configuration from file
read_data waternpt.txt
#read_restart restart.*
#Mass relative mass of atoms
mass 2 15.99943
mass 1 1.00794
group oxygen type 2
group hydrogen type 1
set group oxygen charge -0.8476
set group hydrogen charge 0.4238
#Define potential type
pair_style lj/cut/coul/long 10.0 12.0
kspace_style pppm 5.0e-5
kspace_modify mesh 36 36 36 order 5
#Lennard-Jones Parameters
pair_coeff 2 2 0.0067371579 3.166
pair_coeff 1 1 0.0000000000 0.000
pair_coeff 1 2 0.0000000000 0.000
bond_style harmonic
bond_coeff 1 19.512 1.0
angle_style harmonic
angle_coeff 1 2.3848 109.47
group water type 1 2
velocity all create 373 234324 dist gaussian mom yes rot yes
neighbor 2.0 bin
neigh_modify delay 0 page 200000 one 4000
#minimize 0 0 1000 10000
thermo_style custom step pe ke etotal temp press vol xlo xhi ylo yhi zlo zhi
#Applies or “fixes” NVT MD
fix 1 water shake 0.0001 20 500 b 1 a 1
fix a all nve
#Dumps output files and thermodynamic properties
dump 1 all atom 1000 dump.waterNPT5
thermo 500
#Timestep is 1 fs (0.001 ps)
timestep 0.002
#Number of time steps (reduced)
compute mobile all temp
#fix b all nvt temp 373.0 373.0 1.0
fix b all langevin 373 373 1.0 48279
fix_modify b temp mobile
run 100000
#unfix b
#fix a all temp/berendsen 373 373 100
#fix_modify a temp mobile
#run 500000
#fix b all langevin 373 373 100.0 48279
#fix_modify b temp mobile
compute baro all pressure mobile
fix jsb water press/berendsen iso 1.013 1.013 1000
#fix jsb water press/berendsen xyz 1.013 1.013 1000
fix_modify jsb press baro
fix c all ave/time 1 1000 1000 c_baro file press.profile
#unfix jsb
thermo_style custom step pe ke etotal temp press vol xlo xhi ylo yhi zlo zhi
run 10000000