On 29/10/2010 7:50 PM, vinothkumar mohanakrishnan wrote:
Hi Mark
How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more
clearly? It will be of more useful to me to understand the concept.
It's a pretty basic one in scientific measurement. See
http://en.wikipedia.org/wiki/Error_bar and links thereon, or an
introductory physics text.
When we make a measurement, that's only an estimate of the true value.
When someone cites a range of uncertainty, they are acknowledging that
there is an appreciable chance that the true value, of which they have
taken an error-prone measurement, lies somewhere in a given range. So if
7 +/-500 acknowledges that the true value could lie anywhere from about
-493 to 507, then that's not much less useful than an observation of 1
+/- 500, which acknowledges that the true value could lie anywhere from
about -499 to 501. The details of that chance will vary with exactly
what variation quantity is being reported (standard deviation, standard
error, maximum deviation, quartile, etc.).
Here, g_energy is effectively reporting that the instantaneous pressure
values varied over a range of many hundreds of bar, and that you haven't
made enough observations to report a reliable average.
Mark
One more thing, density (from g_energy command) of water is found to
low (expected 1000) after NPT is equilibration. why? given below is my
average density value. Can i proceed with this density value?
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Density (SI) 979.37 14.3238 14.2431 -0.0525784
-5.25789
Regards
Vinoth
On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:
I am using the semiisotropic pressure scaling because i want the
box size to remain the same as that of the original box size in X
and Y axis and want to change it only on the Z axis. I am doing
this because at a latter stage i want to create an interface with
organic solvent where i need the cross sections (X and Y axis
length) of both the box should be the same.
what i should do now get the pressure of 1 bar?
7 +/- 500 *is* approximately 1 bar, and hardly any better an
approximation than 1 +/- 500. If you want lower fluctuations, use
a larger system and run for a much longer time. Or, since you'll
have to re-equilibrate once you combine the solvent boxes, don't
bother.
Mark
Has no one has got the pressure of water to be close to 1 bar in
GROMACS till now?
Regards
Vinoth
On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote:
Hi Mark
I read the link before posting the question. even though
the fluctation
is between 500-600 (as said in the link) bar the average
pressure is
around 7.4 bar. my concern is the average pressure?.
Because at a latter
stage i am going to combine this water box with another
organic solvent
and i want to avoid any complications there.
Think again of what you just wrote. Your value is 7 +/- 500.
In fact according to normal statistical rules you should
round the value of 7 to 0. If you want more accurate number
you could increase the box size by a factor of 100.
By the way, why are you using semiisotropic pressure scaling
in a water box?
Regards
Vinoth
On Fri, Oct 29, 2010 at 12:22 PM, 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 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote:
Hi Gromacians
I want to do equilibration of water (spc model)
first in the NVT
ensemble and then in the NPT ensemble to maintain
a temperature
of 300K and a pressure of 1 bar respectively. The NVT
equilibration works fine and the average
temperature turns out
to be 299.229 K.
Energy Average RMSD
Fluct.
Drift Tot-Drift
------------------------------
-------------------------------------------------
Temperature 299.229 10.3092
10.2463
0.0393873 3.93877
Heat Capacity Cv: 12.494 J/mol K (factor =
0.00118698)
when i do NPT equilibration i am not getting the
desired
pressure as 1 bar or atleast close to 1 bar
(between 1-1.4 bar).
In the mdp file i used semiisotropic pressure
coupling type
because i want to fix the length of the box same
on two axis as
that of the original box size and want to change
it only on one
axis. can any one tell me why iam not getting the
desired
pressure of 1 bar?.
This looks normal for a smallish water system over
100ps. See
http://www.gromacs.org/Documentation/Terminology/Pressure
Mark
Energy Average RMSD
Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Pressure (bar) 7.4339 574.052
573.574
0.812129 81.2138
Given below is my mdp file (NPT equilibration).
any help is
highly appreciated.
title = DCE NVT equilibration
cpp = usr/bin/cpp
integrator = md
nsteps = 100000
dt = 0.001
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
ns_type = grid
nstlist = 1
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
pme_order = 4
fourierspacing = 0.16
pbc = xyz
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 0.5
ref_p = 1.0 1.0
compressibility = 0.0 4.5e-5
DispCorr = Enerpres
gen_vel = yes
gen_temp = 300
gen_seed = 173529
Regards
Vinoth
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