Yousung Jung wrote:
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?
First make sure your system does not have angular velocity and set
comm_mode = linear
Second run in double precision without cut-off
Third, set shake tolerance to 1e-8 or increase lincs_order
Using the things above you can still use 2 fs time steps.
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
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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