Elisabeth wrote:
Hello,
Thank you. I am looking at potential energies to calculate vaporization
heat. I wanted to know how the fact that berendsen does not lead to
correct ensemble is affecting total potential energy of the system. I
have an unclear image of "correct ensemble". Does this mean whatever
output I am getting from my runs are unreliable?
The Berendsen coupling algorithms produce very narrow distributions of
temperature and pressure. These do not correspond to the correct distribution
of a true statistical mechanical ensemble; plot a histogram and you'll find that
the results are shockingly different between Berendsen and, say, Nose-Hoover for
T. Therefore, the ensemble you're using to measure your properties is not NPT
(or NVT, in the case of thermostat only), it's something undefined and likely
not real. Applying better thermostats and barostats that have been shown to
produce the correct distributions is more rigorously correct.
The effects are usually not terribly noticeable unless you go looking for them.
You'll find that the Berendsen algorithms quite faithfully give you the target
T and P that you desire (which does make them very good for initial
equilibration) and so you naturally assume that everything is fine. While
that's all well and good in one sense, the fluctuations of T (and thus
velocities, and thus kinetic energy) are wrong. If KE does not fluctuate
properly, then neither does PE (since you're then affecting energy flow between
PE and KE, while total energy stays fixed, in theory).
The larger point is that if you claim to apply an NVT (or NPT) ensemble using
Berendsen coupling, you're not correct, strictly speaking.
-Justin
Appreciate any clarification.
Thank you,
Best,
On 15 August 2011 19:34, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 16/08/2011 7:05 AM, Elisabeth wrote:
Dear all,
I noticed that applying Parrinello-Rahman (PR) pressure coupling
even after equilibration with berendsen does not lead to target
value for pressure when
; Bonds
constraints = none
is used.
The use of constraints and the integration step size is linked.
Roughly speaking, no constraints should accompany a 0.5 fs time
step, H-bond constraints with 1fs and all constraints with 2fs.
Haphazard changes to .mdp files have all kinds of these "gotchas".
I tried Berendsen for to get fixed pressure ( 50 bar) but in the
next run PR even for long time is giving 52 bar. This is the case
for other target pressures too.
You need to be sure to collect statistics only after equilibration,
and consider whether the observed variation is consistent with
convergence to a given value.
So this made me select Berenden which is giving target pressure
values but my concern is whether my results are reliable because
BR does not give the exact ensemble as PR. I read somewhere on the
list that fluctuation properties can not be calculated when BR is
used. What does "fluctuation property" mean?
BR does not produce the correct ensemble. I forget the details about
why, but there are references in the T-coupling section of the
manual you should consider.
Does this mean that any property calculated form fluctuations of
some other quantity can not be obtained>? like heat capacity which
is defined based on enthalpy fluctuations?
IIRC, yes.
I am interested in potential energy terms (g_energy bonded/non
boned terms)
I routinely struggle to see why people think they can learn anything
from these.
and structural properties like rdf for a number of polymer
molecules, system size around 3000 atoms.
Thank you for your comments.
Best,
constraints = none
; Run control
integrator = md
dt = 0.001
nsteps = 5000000
nstcomm = 100
nstenergy = 100
nstxout = 100
nstlist = 10
ns_type = grid
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.25
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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