Re: Temperature dependent unfolding..

From: Arun Krishnan (
Date: Wed Sep 05 2007 - 11:40:56 CDT

Hi Peter,

Thanks for pointing out that I wasnt doing an NPT equilibration run...
forgot to turn on LangevinPiston. As for progressive unfolding.. yes I do
see some unfolding.. but nowhere near as drastic as seen in that paper...Let
me retry by equilibrating at 520K with NPT and then doing a 2ns production
run.. shall get back to you all after that.

Again, thanks a lot to everyone for your help.



On 9/6/07, Peter Freddolino <> wrote:
> Hi Arun,
> rather silly of me; you can also read the volume directly from the log
> file. Nevertheless, there's a 1.4x increase in system volume that
> occurs during your production run, which is fairly significant. Out of
> curiosity, is there any reason you didn't also equilibrate at 520K in
> NPT? The config file you posted has the piston turned off, although your
> simulation summary listed this as NPT. It's probably not ideal to have
> such a large volume adjustment occur during a production run.
> I don't see any serious problems in your simulation that would lead to
> wrong results though. Unfortunately, there isn't quite enough
> information in the methods section of that unfolding paper you're
> comparing your results with to ensure that you're using identical
> conditions; certainly the system size is different, and they don't
> mention the thermostat or barostat being used, for example. Do you see
> any kind of progressive unfolding in your simulations, even if it is
> slower than the 1 ns they reported?
> Best,
> Peter

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:12 CST