RE: Why does my volume suddenly expand as I increase temper ature.. .

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Tue Nov 12 2013 - 09:14:29 CST

Thanks! That makes a lot of sense. Quick question though, would this be a more advisable way to do this simulation versus just removing the barostat and keeping constant volume?

Thanks a lot for the help,
Erik
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Norman Geist [norman.geist_at_uni-greifswald.de]
Sent: Tuesday, November 12, 2013 1:23 AM
To: 'Aron Broom'
Cc: Namd Mailing List
Subject: AW: namd-l: Why does my volume suddenly expand as I increase temper ature.. .

Using antoines equation you should be able to compute the correct target pressure for your temperature. Itís also possible to update it due tcl scripting if you change temperature during simulation.

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Aron Broom
Gesendet: Dienstag, 12. November 2013 02:13
An: Martin, Erik W
Cc: NAMD Mailing list
Betreff: Re: namd-l: Why does my volume suddenly expand as I increase temperature.

I think that normally if one is using temperature to melt things or for say replica exchange, you would do constant volume, i.e. NVT, rather than constant pressure, i.e. NPT. I may be wrong. Of course, the TIP3P water model isn't meant for phase transitions, but one would still expect something of that sort at some temperature once the kinetic energy overcomes the attractive potentials. So I would think what you saw at ~550K was TIP3P "boiling".
Probably a good bet would be to check out what people do with replica exchange (maybe NVT as above), since they would need to solve similar problems.
~Aron

On Mon, Nov 11, 2013 at 6:55 PM, Martin, Erik W <Erik.Martin_at_stjude.org<mailto:Erik.Martin_at_stjude.org>> wrote:

So, I have set up simulations where every 2 nanoseconds I increase the temperature by ten degrees. The goal of this simulation was to attempt to "melt" structures that had previously formed at constant temperature. It is possible that I went about this in a rather naive way, and would appreciate any insight.

I accomplished this by simply rescaling velocities and resetting Langevin Temp and Piston Temp to the current temperature in a short tcl script. I did not anticipate that the volume would be static in these simulations, but was a bit surprised by what I saw.

The simulation seemed to progress fine with actually very little change in Volume until it got to 550 degrees. At this point I saw a sudden explosion in volume accompanied by a drop to near zero pressure. These jumps appear to also include a sudden increase in total energy. I've never done this sort of thing before and am not sure what I am actually seeing happen.

If anyone can interpret this for me, I'd greatly appreciate it.

-Erik

PS. This is a simulation in TIP3 water of ~90k atoms.

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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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