Elisabeth wrote:
Thanks Justin for your thorough description. Is there any specific tool
in gromacs to plot histograms or you mean I follow the customary
plotting procedure?
You have to write your own code from, e.g., g_energy output.
I have one more question. I am now trying using PR pressure scheme with
v-rescale thermostat for NPT dynamics. Before dynamics run, can I apply
berendsen barostat combined with v-rescale thermostat to equilibrate or
since I am using berendsen barostat, T coupling scheme has to be also
berendsen?
You can use any combination you like during equilibration.
-Justin
Thanks,
On 16 August 2011 13:17, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Elisabeth wrote:f
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>
<mailto: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 <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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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