VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jan 09 2010 - 03:37:49 CST

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