From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 21 2010 - 08:15:10 CST
On Thu, Jan 21, 2010 at 8:29 AM, jose correa <corrjose_at_gmail.com> wrote:
> Dear all
> We are trying to unfolding a protein employing thermal conditions (300, 400,
> 500 and 600 K). I was thinking that at 600 K the protein was unfolded, but,
i assume that you are aware of the fact that at 600K parameters
that were derived for 300K have limited applicability.
> it did not happen. I start heating the sytem from equilibration and then, I
> matain the system under NTV. Do you have any suggestion?.
how long did you run? what kind of system? how large of a protein?
how large is your solvation box relative to the size of the protein?
depending on the rigidity of your system, it may take a while to break up
a structure. also you need to allow for fluctuations, i.e. give the protein
some "wiggle room" to ease the process.
> Best wishes
> José Correa-Basurto
> ESM-IPN, México
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:21 CST