My system is a water/methanol mixture with 100 and 300 molecules for water and methanol, respectively. I equilibrated the system with pbc for 500 ps at 300K in vacuum. Then, I ran the actual simulation at 235K in vacuum WITHOUT pbc to simulate a droplet of the mixture. I see a few water and methanol molecules escaping "the system" (or, the droplet) during the simulation.
The problem that I am struggling with for this system is, after about 400 ps of the actual dynamics at 235K, temperature starts fluctuating badly, getting worse until the simulation stops at around 600 ps. When I visualize the trajectory, I see the system (a droplet in vacuum) rotating and translating at around the same time as the temperature begins fluctuating. I did use comm_mode = angular to eleminate rot. and trans. modes.
I reduced the time-step to 0.5 fs, but the problem still exists (the system translating significantly in vacuum). Is it possible that this is due to the fact that the center of mass is used for removing translational and rotational motion and a few escaped molecules are causing this problem? (If those ones that are escaping are causing the problem, I guess I could use pbc with a "big" box.) Assuming this is the case, I have two questions:
1. Is there a way to fix this rotational and translational artifact without using pbc for my system?
2. If I have to use pbc, what would be the most economic combination in terms of box size and etc?
Thanks very much for your help!
Yousung
ps. I am attaching my mdp file below, and an xvg file for temperature analysis.
----------------
integrator = md
tinit = 0.0
dt = 0.001
nsteps = 1000000
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstlist = 0
energygrps = System
ns_type = simple
pbc = no
comm_mode = angular
; Constraints
constraints = all-bonds
constraint_algorithm = lincs
;Treatment of Vdw and Elctrostatics
vdwtype = cut-off
coulombtype = cut-off
rlist = 0
rvdw = 0
rcoulomb = 0
; Temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1
tc-grps = System
ref_t = 235
; Pressure coupling is off
Pcoupl = no
; Generate velocites is on at 235K
gen_vel = yes
gen_temp = 235
gen_seed = 173529
energy.xvg
Description: Binary data
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