CCL: NPT TIP5P, 1atm MD

Sent to CCL by: Manish Agarwal [zmanish|*|gmail.com]
Dear CCLers

Excellent suggestions, that too on the weekend ... My thanks to all.
I should have mentioned that I am using cubic Periodic Boundary.

Here is what I intend to do:

The time step of 1 fs is, in my opinion, not too low or too high for
bulk water simulations at temperatures where there are no slow
dynamics.
>> Even more, you can increase up to 2 fs for larger time consumption, another thing is that you can use "Rattle" or "Shake" algorithms to save your computation time...
I _am_ going to increase the number of molecules, and see if it
changes the outcome - 500, and 1000.
I am also going to increase the number of simulation timesteps - 4-6
million should suffice for the test. I will also try Nose-Hoover
thermostat-barostat combination.

In the past I have run Berendsen NVT simulations with tau=200ps with
no problems - although, reviewers have complained it to be 'too high'.
The large relaxation time allows for internal dynamics to be as near
NVE as possible, specially near temperatures below the model's melting
point. But this is my first brush with NPT.
>>It's abnormally too high,
My main concern has been that I am trying to compare MD-NPT results
with those obtained from MC-NPT.
>> in long times,according to ergodicity hypothesis, you will come to nearly same results
I will try and post my results in the next 24-48 hours...

Looking forward to more discussion,
Regards, and thanks again.
Manish Agarwal
- - - - - - - - - - - - - - - - - - - - - - - - - - -

On 6 February 2010 23:02, Venable, Richard (NIH/NHLBI) E
venabler!A!nhlbi.nih.gov <owner-chemistry . ccl.net> wrote:
>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*-nhlbi.nih.gov]
> I have to disagree.
>
> If there are suspected stability problems, the last thing one should do is to increase the timestep.
>
> The weak coupling scheme typified by the Berendsen thermostat and barostat have been justly criticized by many, including Allen and Tildesley; Nose-Hoover extended system approaches are regarded as considerably less flawed.
>
> Starting from 0 K is usually not necessary, and can be ill advised in some programs. Anything below 200 K should be just fine.
>
> I don't believe one can run NPT without periodic boundaries.
>
> --
> Rick Venable
> compuational chemist
>
> ________________________________________
>> From: owner-chemistry+rick_venable==nih.gov||ccl.net [owner-chemistry+rick_venable==nih.gov||ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.ibrahim[a]compchem.net [owner-chemistry||ccl.net]
> Sent: Saturday, February 06, 2010 11:17 AM
> To: Venable, Richard (NIH/NHLBI) [E]
> Subject: CCL: NPT TIP5P, 1atm MD
>
> Dear Manish
> I am not familiar with DL Ploy.
> But, if you don't mind, you can have a go with the following issues to reproduce the water density:
> * Use NPT ensemble with relaxation time of 2.0ps
> * Use Berendsen Thermostat with 0.5ps time constant
> * Use Periodic Boundary Condition (Important)
> * If it is available, start your run from 0K and increase the temperature gradually until reaches 300K. (During heating step, use constant volume boundary condition).
>
> Have a go with these issues, Good look
> Sincerely;
> M. Ibrahim
>
>
> On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com<http://gmail.com> <owner-chemistry{=cl.net<mailto:owner-chemistry{=cl.net>> wrote:
>
> Sent to CCL by: Manish Agarwal [zmanish^^gmail.com<http://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<http://gmail.com" target="_blank">http://gmail.com>>
>
>
>
> -= This is automatically added to each message by the mailing script =-
> E-mail to subscribers: CHEMISTRY{=cl.net<mailto:CHEMISTRY{=cl.net> or use:E-mail to administrators: CHEMISTRY-REQUEST{=cl.net<mailto:CHEMISTRY-REQUEST{=cl.net> or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt" target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
>
>
> - This is automatically added to each message by the mailing script -> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt>
>
>

-= This is automatically added to each message by the mailing script =-
To recover the email address of the author of the message, please change
the strange characters on the top line to the %% sign. You can also
look up the X-Original-From: line in the mail header.

E-mail to subscribers: CHEMISTRY%%ccl.net or use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST%%ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/