Fwd: deca-alanin folding by remd parallel tempering

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Sep 04 2013 - 04:35:45 CDT

In other words, is folded alanin.pdb from experiments or from parallel
tempering or other forms of remd simulations? Just to know to what I am
comparing the results of my parallel tempering with provided alanin.pdb.

It should be clear that I am running the same simulations on the
polipeptide of my interest. Is there a tool for carrying out a clustering
of conformations from parallel tempering?

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Sep 4, 2013 at 8:40 AM
Subject: deca-alanin folding by remd parallel tempering
To: namd_at_ks.uiuc.edu

I asked yesterday, perhaps masked by inappropriate subject:

from where "alanin.pdb" originates, by referring to the example of
deca-alanin folding by pure parallel tempering in namd2.9 manual. I run the
example by providing "unfolded.pdb" and no alanin.pdb (which is included in
the example). I got all eight replicas and VMD graphics for them according
to show_replicas.vmd. Is the folded structure "alanin.pdb" to be derived
from these replicas? Or what else?

It seems that a previous related question:

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My name is Jun Zou and I'm a graduate student in Sichuan University, and I
have use NAMD for some times. The replica exchange simulation is now
available in NAMD 2.6. There is a Tcl variables "*fit_pdb_file*" (
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node40.html) which I don't
understand its usage. I was wondering whether it's just for easily view in
VMD or it has impact on our replica exchange simulations' results. Thanks
for your help!

was never answered. Does that mean that the issue should be self clear?
Unfortunately, that is not with me.

thanks for advice

francesco pietra

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