Re: SMD Energy

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Tue May 30 2006 - 13:50:28 CDT

As Lewyn suggested, you need to be very careful about the energy. I
think the most important question you need to ask now is: what do you
hope to say about your system by calculating the total energy
difference? Beyond ensuring that the MD is working properly (by
checking total energy conservation in NVE), I have never found the total
energy to be very useful in studying large biosystems.

Also, I assume you're using a Langevin thermostat? In this case, you're
going to have large fluctuations in the energy anyway, and it may not be
practical to determine the total energy difference (this applies any
time you have a Langevin thermostat: NVT or NPT). How does the
difference between initial and final energies compare to the energy
fluctuations?

-Sterling

Pijush Ghosh wrote:

> Dear Li and Sterling
>
> I appreciate your discussion. Well as Li mentioned that the heights
> of the peaks depends on the rate of pulling. I have seen similar
> response for my system too. I want to share some result on energy with
> you all so that we can have some more discussion. I am doing at NPT
> ensemble. I observed at all velocities the difference in total energy
> between final and initial is much higher than the area under the
> Force-Displacement curve. Is it expected ?
>
>
>
> Pijush Ghosh
>
> PhD Student
>
> Department of Civil Engineering
>
> North Dakota State University
>
> Fargo. ND. 58105. USA
>
> Phone:
>
> 701-231-6491(Lab)
>
> 701-231-4341(Res)
>
> ------------------------------------------------------------------------
>
> *From:* Lewyn Li [mailto:ll2150_at_columbia.edu]
> *Sent:* Tuesday, May 30, 2006 12:01 PM
> *To:* Pijush Ghosh
> *Subject:* Re: namd-l: SMD Energy
>
>
>
> Dear Pijush,
>
>
>
> This is an interesting question. In my opinion, this
> depends on how fast you are pulling the protein. I have found that
> pulling a protein from its ends more quickly generally resulted in
> higher force peaks. If you then just integrate the force over the
> extension, you would get a larger number for a faster pulling. The
> papers by Lu & Schulten on pulling I27 shows this effect quite nicely.
>
>
>
> Also, I believe (but I am not certain) that we need to be
> careful about the "energy" in SMD. As the force is calculated from the
> moving harmonic potential well, I think the energy of the well should
> be taken into account in some way when we speak of the "energy" of the
> system.
>
>
>
> Any advice and suggestions from the SMD experts out there??
>
>
>
>
>
>
>
> LEWYN
>
>
>
> On May 30, 2006, at 11:47 AM, Pijush Ghosh wrote:
>
>
>
> Dear SMD Experts
>
> In NAMD and from concept of statistical mechanics is it logical to
> conclude that the area under the Force-Displacement curve for a
> protein is equal to the difference in the initial (t=0) and final
> (t=T) total energy(bonded + nonbonded) ?
>
> I would appreciate any discussion on this.
>
> Pijush Ghosh
>
> PhD Student
>
> Department of Civil Engineering
>
> North Dakota State University
>
> Fargo. ND. 58105. USA
>
> Phone:
>
> 701-231-6491(Lab)
>
> 701-231-4341(Res)
>
>
>
>
>

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