From owner-chemistry@ccl.net Sun Feb 7 00:09:00 2010 From: "Amir Taghavi amir_taghavi14__yahoo.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41198-100206144101-15502-gaNt/bIrLhW/QgQiSOzzeQ(a)server.ccl.net> X-Original-From: Amir Taghavi Content-Type: multipart/alternative; boundary="0-190973887-1265485235=:14825" Date: Sat, 6 Feb 2010 11:40:35 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Amir Taghavi [amir_taghavi14%a%yahoo.com] --0-190973887-1265485235=:14825 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --- On Sat, 2/6/10, Amir Taghavi wrote: > From: Amir Taghavi Subject: Re: CCL: NPT TIP5P, 1atm MD To: "CCL Subscribers" Date: Saturday, February 6, 2010, 4:13 PM 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= ,=20 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 conv= erge 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 converg= es 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, th= en 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 th= e real ones. Hope this is helpful. Regards, Amir Taghavi Nasrabadi,Tehran Univ. --- On Sat, 2/6/10, Manish Agarwal zmanish**gmail.com wrote: > From: Manish Agarwal zmanish**gmail.com Subject: CCL: NPT TIP5P, 1atm MD To: "Taghavi, Amir " 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=A0 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 -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-190973887-1265485235=:14825 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


--- On Sat, 2/6/10, Amir Taghavi <= i><amir_taghavi14 a yahoo.com> wrote:

From: Amir Taghavi <amir_taghavi14 a yahoo.com>
Subject: Re: = CCL: NPT TIP5P, 1atm MD
To: "CCL Subscribers" <chemistry a ccl.net><= br>Date: Saturday, February 6, 2010, 4:13 PM

<= style>

Hi Dear Manish,

In order to work in an NPT ensemble, you have to con= sider this that at higher times the system will converge to your desired pressure= ,

As usual, working in NPT ensemble has its own diffic= ulties, you have to monitor the pressure fluctuations, and then if you average of pressure values, you will see that your pressure average smoothly will conv= erge to your desired value at higher durations of time, while saving its fluctuations.

I observed your tau-values and thermostats and baros= tats, you have chosen good ones, the experience has shown that the better converg= es in 0.5 ps of tau-pressure,

But I recommend you strongly use the higher number o= f water molecules (i.e. at least 500 molecules).

In fact to work in such a system, you have to monito= r the total energy and pressure values to ensure that reaching to equilibrium, th= en 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 t= he real density in experimental, as all of these water molecules are models, not th= e real ones.

Hope this is helpful.

Regards,

Amir Taghavi Nasrabadi,

Te= hran Univ.



--- On Sat, 2/6/10, Manish Agarwal zmanish**gmail.com <own= er-chemistry a ccl.net> wrote:

Fro= m: Manish Agarwal zmanish**gmail.com <owner-chemistry a ccl.net>
Sub= ject: CCL: NPT TIP5P, 1atm MD
To: "Taghavi, Amir " <amir_tagh= avi14 a yahoo.com>
Date: Saturday, February 6, 2010, 6:27 AM


Sent to CCL by: Manish Agarwal [zmanish^^gmail.co= m]
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 Therm= ostat and Barostat
Nose-Hoover Thermostat and Barostat

am using E= wald summation for electrostatics,
256 water molecules. 2000000  st= eps, with or without velocity scaling
in the beginning 1fs time step
DLPOLY ver 2.19

The problem is as follows : either the pres= sure does not stabilize at
1atm (too low or too high) or the temperature= does not maintain at
300K
When both are maintained, for example Bere= ndsen 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 mea= n).

In the NVT ensemble, however, I have been able to reproduce othe= r
static(orientational order) and dynamic properties(diffusivities) - so=
the model seems fine.

Any thoughts, suggestions are appreciated.=

Regards,
Manish Agarwal
<zmanish||gmail.com>


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