Fwd: replica exchange and colvars

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jul 31 2013 - 02:49:11 CDT

Addendum: I am not concerned with r saving computing time (freezing
most protein with colvars will save little, if any, time), rather with
what will occur to the "non mobile" part of the protein well described
by x-ray diffraction. Could temperate tempering also help refyining
the whole structure in explicit solvent?

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Jul 31, 2013 at 9:34 AM
Subject: namd-l: replica exchange and colvars
To: NAMD <namd-l_at_ks.uiuc.edu>

I would like to try to model the scarcely structured - presumably
involving low energy barriers - portions of a protein with parallel
tempering. I hope that clustering reveals a dominant situation.

Stated that the mobile parts are about 5% of the total - highly
titrable - protein multimer, and that a bilayer membrane and TIP3
water box are in place, is it advisable to carry out parallel
tempering while restraining with colvars all protein except the mobile
parts I want to model? I am new to parallel tempering, and cannot
assess it in house because namd requires more than one physical node,
which is not the case of my shared mem GPU machine.

thanks for advice

francesco pietra

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