[gmx-users] phase transition in MD simulation
Dallas.Warren at monash.edu
Wed Sep 14 04:09:42 CEST 2011
It certainly is, you just need to focus on a property that changes between the phases and that is obtainable from the MDSs. For a transition from liquid to solid, things like RDF, SDF, dihedral fractions and diffusion coefficients might provide some insight.
You have the trajectories, why don't you just try as many of the properties you can get out of it and see if you see a change?
Visual inspect is also a powerful technique, but you will need to back that up with some actual values. The averaging function in VMD can be quite handy for this, showing the "average structure" of a molecule over a particular time frame.
Something you need to consider, is the time frame involved for a polymer to change between a liquid and "solid" state and the simulation time you have used. With having no idea on what polymer you have, size etc, I would hazard to say you would need easily something in the order of 200+ns to start to see some ordering occurring, if not something an order of magnitude longer. Polymers are big molecules and it will take long time for things to rearrange.
And finally, the forcefield wont necessarily show the correct behaviour, unless it was derived to do that. It could simply be a poor model to use for showing phase behaviour.
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Elisabeth
Sent: Wednesday, 14 September 2011 11:33 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] phase transition in MD simulation
I am working on a pure polymer melt system under NPT and at a given T, pressure is increased up to around 1000 bar. However, the phase diagram of the polymer is indicating that at this T, as pressure is increased to above 500 bar, system falls below the melting point.
I mean I am doing NPT on a liquid polymer by packing the chains in to the box but even applying a pressure of 1000 bar does not make the atoms or chains resemble a solid phase. The system would only become a more packed liquid phase. In other words, MD is representing an extrapolated liquid phase in the subcooled region.
My question is whether there is any way to identify phase transition from MD simulation.
Please comment and let me know what you think.
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