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Hi Dear Manish,
In order to work in an NPT ensemble, you have to consider
this that at higher times the system will converge to your desired pressure,
As usual, working in NPT ensemble has its own difficulties,
you have to monitor the pressure fluctuations, and then if you average of
pressure values, you will see that your pressure average smoothly will converge
to your desired value at higher durations of time, while saving its
fluctuations.
I observed your tau-values and thermostats and barostats,
you have chosen good ones, the experience has shown that the better converges
in 0.5 ps of tau-pressure,
But I recommend you strongly use the higher number of water
molecules (i.e. at least 500 molecules).
In fact to work in such a system, you have to monitor the
total energy and pressure values to ensure that reaching to equilibrium, then
taking average of water density for those durations, finally you find that your
density has been nearly reached up to the desired value,
Of course you should not have expected to reach to the real
density in experimental, as all of these water molecules are models, not the
real ones.
Hope this is helpful.
Regards,
Amir Taghavi Nasrabadi, Tehran
Univ.
--- On Sat, 2/6/10, Manish Agarwal zmanish**gmail.com
<owner-chemistry a ccl.net> wrote:
From: Manish Agarwal zmanish**gmail.com <owner-chemistry a
ccl.net>
Subject: CCL: NPT TIP5P, 1atm MD
To: "Taghavi, Amir "
<amir_taghavi14 a yahoo.com>
Date: Saturday, February 6, 2010, 6:27
AM
Sent to CCL by: Manish Agarwal
[zmanish^^gmail.com] Dear CCLers, I am having trouble reproducing the
density at 1 atm, 300K for TIP5P water, or for that matter any water model in
the NPT ensemble using Molecular Dynamics: have tried Berendsen
Thermostat and Barostat Nose-Hoover Thermostat and Barostat am using
Ewald summation for electrostatics, 256 water molecules. 2000000 steps,
with or without velocity scaling in the beginning 1fs time
step DLPOLY ver 2.19 The problem is as follows : either the pressure
does not stabilize at 1atm (too low or too high) or the temperature does not
maintain at 300K When both are maintained, for example Berendsen
Thermostat relaxation time 0.1ps, Barostat relaxation time 0.5ps, the density
does not reach 0.99g/cc; also, the energy profile with time looks too
perturbed (does NOT look like a nice fluctuation about the mean). In
the NVT ensemble, however, I have been able to reproduce
other static(orientational order) and dynamic properties(diffusivities) -
so the model seems fine. Any thoughts, suggestions are
appreciated. Regards, Manish
Agarwal <zmanish||gmail.com> -= This is automatically
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