[gmx-users] mdrun in vacuum diverging? -- possibly due to nopbc?

Yousung Jung yousung at gmail.com
Sun Mar 5 05:01:20 CET 2006

Dear more experienced users,

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!


ps. I am attaching my mdp file below, and an xvg file for temperature


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
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