help requested

From: Sridhar Vaddadi (
Date: Wed Sep 23 2009 - 11:23:36 CDT

Dear Community,
I am planning to run a NAMD simulation on HIS-ARG peptide. I have XYZ coordinates of this system. Can any one suggest how to generate pdb and psf files from this XYZ system. Is, VMD a good help to do this. Your suggestions are really appreciated.
Sridhar Vaddadi


From: on behalf of Rick Calloway
Sent: Tue 9/22/2009 12:08 PM
Subject: namd-l: Precision of Coordinate data

Hi community,
Can someone help me better understand the precision of the output coordinate data.
I am looking for statistically significant movement of the center of mass of a large molecule. Using VMD's measure center command returns angstroms out to 15 decimal places and looks quite tempting.
If the last 12 or so decimal places had meaning I could significantly reduce the runtime for my system.
How can I determine how many of these digits are significant?
Thank you in advance.
Rick Calloway

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