Re: Temperature dependent unfolding..

From: Arun Krishnan (
Date: Thu Sep 20 2007 - 20:24:52 CDT

Hi Neema,

Thanks for your input. I basically wanted to respond only after trying out
what you had suggested. I want to put down my experience here in the hope
that anybody else who wants to use NAMD for temperature-dependent folding
won't have to spend a frustrating couple of months while doing that. To
recap, here are the steps I did:

a) Energy minimization of protein in water box
b) Heating to 300K (in steps of 0.1K/fs)
c) Equilibration at 300K for 50ps - NPT @1atm - 1fs time step
d) production run @300K for 1ns, NPT @1atm, 2fs time step
e) Heating to 520K (in steps of 0.1K/fs)
f) Equilibration at 520K for 50ps - NPT @30bar - 1fs time step
g) production run @52K for 8ns, NVE, 1fs time step

Basically, what you have suggested does work. The time scales for unfolding
are different than those observed in other works but the unfolding pathway
is the same (which is a relief).

Again I thank all of you for your help.



On 9/8/07, Neema Salimi <> wrote:
> Arun,
> I equilibrated at 500K and ~30 bars, then switched to NVE after the system
> stabilized.
> Richard,
> While your criticism may be valid, it is by no means helpful. Arun is
> interested why ubiquitin isn't unfolding in his simulations, not whether
> it's the right thing to do. If you don't have some insight to offer to the
> list on this topic, perhaps you shouldn't clog up everyone's inbox.
Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Phone: +81 (0)235-29-0824

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