VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jan 09 2010 - 16:01:21 CST
- Next message: Jacob Poehlsgaard: "Maestro file export"
- Previous message: Christine Horejs: "display surface amino acid beads"
- In reply to: Francesco Pietra: "obscurity in sbcg tutorial description"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
I have removed the obscurity. Thread closed
fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Jan 9, 2010 at 10:37 AM
Subject: vmd-l: obscurity in sbcg tutorial description
To: vmd <vmd-l_at_ks.uiuc.edu>
As to the sbcg tutorial, It is not clear to me how the
<aa_ref-monomer-noh.dcd> file was obtained. I assume from the
description that the MD simulation was carried out on the all-atom
<monomer.pdb> and then the .dcd file was curtailed of hydrogen
information.If so, may I ask how to do that? If not, please add a few
words on how todo.
The reason is that by using (on a different model; I did not try the
tutorial itself for the above reasons) file .dcd with H information
(and therefore the corresponding file to aa_ref_monomer-noh.psf with
all H information), the 4th and 5th columns in the resulting .dat
files turn out to have all <0> and all <inf>, respectively. No
problems for the cg simulation (iteration1).
Thus, if I am not dropped into major mistakes, the <noh> is a major
obscurity in this tutorial. It impedes application to other models
(which is the very interest of a reader)
thanks
francesco pietra
- Next message: Jacob Poehlsgaard: "Maestro file export"
- Previous message: Christine Horejs: "display surface amino acid beads"
- In reply to: Francesco Pietra: "obscurity in sbcg tutorial description"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]