On 31/10/2010 8:17 PM, Tsjerk Wassenaar wrote:
Hey,
There's quite a number of people that should be rereading their statistics... :p
First of all, there are instantaneous measurements, averages and
fluctuations. If the statistics (mean/fluctuation) are 7 +/- 500, then
that doesn't mean that the average of 7 is an estimate that may be off
by 500, and the true average can lie between -493 and 507. It means
that the average is 7, but that any instantaneous measurement may be
expected to lie between those values, and that two measurements, say
-300 and +300, can not be expected to be from different distributions.
So a pressure of 300 bar measured in one frame does not suggest that
the pressure of the system is higher than that of a system of the same
constitution with a pressure measured in one frame of -300 bar.
Indeed, I was speaking crudely :-) One wants to measure the actual
standard error (or similar) of average pressure observations over a
given length of time to have proper confidence bounds for the estimate
of the average pressure.
Now the real issue is that the average value (7) is an estimate of the
true mean, which is expected to be 1, as that is given as target
value. The average was determined over a short time, 100ps. Every
interval of 100ps will yield a different value for the observation
'average over 100ps', and these averages will have a certain
distribution around an average 'average over 100ps' observations. If
you do ten of these then the average over averages will still only be
an average over 1 ns, which will be a better estimator of the true
mean value, but is still an estimate itself. And this can be continued
ad infinitum. The average observed over a certain time interval will
converge to the true mean with increasing interval length.
The standard deviation of 'average pressures observed over 100ps' is
likely more than a few bar if the fluctuation in instantaneous values
is so huge. In that regard, an observed average pressure of 7 bar over
100ps is probably consistent with a system at a mean pressure of 1
bar.
Yes.
Mark
Hope it helps,
Tsjerk
On Fri, Oct 29, 2010 at 4:58 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
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>
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> 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>> 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
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
