[gmx-users] Re: Anomaly in Temperature Behavior

[S. Alireza Bagherzadeh]

Dear Dr.Frolov,

Thank you for your response and time.
Please see below.


On Wed, Jan 23, 2013 at 3:00 AM, <gmx-users-request at gromacs.org> wrote:

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>    1. Re: Heme group with CHARMM27 FF (Arvind Kannan)
>    2. Re: help with building DNA in gromacs (Justin Lemkul)
>    3. Re: Anomaly in Temperature Behavior (Andrey Frolov)
>    4. Re: help with building DNA in gromacs (?????)
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> Message: 3
> Date: Tue, 22 Jan 2013 22:34:45 -0800 (PST)
> From: Andrey Frolov <andrey.i.frolov at mail.ru>
> Subject: [gmx-users] Re: Anomaly in Temperature Behavior
> To: gmx-users at gromacs.org
> Message-ID: <1358922885228-5004812.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
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> S. Alireza B wrote
> > During this run we freeze the solid phase in
> > all three dimensions. We then take the final configuration of this run,
> > unfreeze the solid phase, and subject it to a long NVE simulation to
> study
> > the dissociation of the solid phase...
> >
> > ... the temperature keeps increasing which is contrary to the physical
> > fact that the dissociation
> > process is endothermic.
>
> 1) Imagine you have just the solid state at the beginning of the
> simulation,
> which is frozen (no forces are acting on the atoms). Then you unfreeze the
> system, which means you switch on interactions between particles =>
> non-zero
> forces acting on particles appear. Despite the fact that the initial
> velocities were zero, the non-zero forces in few integration time steps
> will
> result in non-zero velocities on the particles, which means that
> temperature
> will increase. So, to my mind, what you observe is not an anomaly. The
> solid
> state in your NVE simulation is far from equilibrium. The quick increase of
> temperature (in ~ 0.5 ps) is due to relaxation of the solid internal
> degrees
> of freedom. I would expect, that no molecules melt to liquid phase in this
> short time. Probably, you should just wait longer until solid starts
> melting
> ?
>
> Actually I ran my NVE for 2ns and T keeps increasing up to about 550K at
2ns.
My concern is that at the end of my 0.5 ns NVT run the T is ~300K; however,
at the first step of my NVE, when no forces has exerted on unfrozen
molecules yet, the T appears to be ~185K!



> 2) Also, I would suggest to prepare your system closer to equilibrium.
> Instead of "freeze" you can use "position_restraints". Also, you can use
> different  temperature coupling bathes to your solid and liquid. Setting
> sufficiently lower reference temperature for the solid phase will prevent
> it
> from melting.
>

This will be an insightful test...
I will run my system with position restraint and will update you in detail
once I finished the run.


>
> 3) Another suggestion, could it be that there is a spontaneous
> crystallization in your system instead of melting ?
>

The output configuration of my system shows that all of my solid phase has
melted. So, no crystallization occurred.


>
> Andrey
> ----
> Andrey I. Frolov, PhD
> Postdoctoral fellow
> Institute of Solution Chemistry
> Russian Academy of Sciences
>
>
>
>
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>
>
>
>


-- 
S. Alireza Bagherzadeh
PhD Candidate
Dept. of Chem. & Bio. Eng.
University of BC
2360 East Mall
Vancouver BC V6T1Z3