Hello all users,
I have been simulating 1000 molecules water system. I’m using TIP3P water model and using lj/cut/coul/long potential to run NPT and then NVT simulation (the units are set to real & I’m setting periodic boundary conditions). After this I save the system to a restart file and later run it with metadynamics. For running metadynamics I’ve been using PLUMED (file attached along with the input script below). The simulation runs perfectly with 1fs timestep but when I try to run the same metadynamics simulation with 2fs timestep, I’m observing large fluctuations in pressure and temperature and can’t obtain gaussian distributed total energy as I do for 1fs.
I’ve tried changing Tdamp for the thermostat but I wasn’t able to get any good results. Would accept any suggestions/feedback on how to make the simulation work with the new timestep.
Thanks,
Nisarg
Input script
read_restart nvt.restart.5000000
kspace_style pppm 1.0e-5
#variables
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+23
variable sysdensity equal v_sysmass/v_sysvol/1.0e-24
variable etotal equal etotal
variable pe equal pe
variable ke equal ke
variable p equal press
variable time equal step*dt+0.000001
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp etotal pe ke
thermo 10
thermo_modify norm no flush yes
fix 3 all nve
fix 4 all temp/csvr 300.0 300.0 100.0 54324
fix 5 all ave/time 100 1 100 v_time c_thermo_temp v_p v_sysdensity v_etotal v_pe v_ke file wte_out.txt
fix 6 all plumed plumedfile plumed.dat outfile p_metad.log
timestep 2
#forces
compute 1 all property/atom fx fy fz
dump 1 all custom 100 force_wte.dump id type fx fy fz
dump_modify 1 sort id
dump 2 all custom 100 water_wte.dump id type x y z
dump_modify 2 sort id
restart 9000000 nvt.restart
run 2500000
Plumed script
UNITS ENERGY=kcal/mol
energy: ENERGY
METAD …
LABEL=metad
ARG=energy
HEIGHT=0.6
BIASFACTOR=32
TEMP=300.0
SIGMA=35
FILE=HILLS
PACE=125
… METAD
PRINT ARG=energy STRIDE=250 FILE=COLVAR