VMD-L Mailing List

From: Aryan Vahedi-Faridi (arvah1_at_morgan.edu)
Date: Sun Aug 02 2015 - 19:30:52 CDT

Hello,

I currently have an issue whereby I need the XST file from a NAMD Energy
Plugin Run. Basically once I have this file I will use the PBCtools to
apply it to a trajectory so that I can get a better contact area curve (see
powerpoint attached).

To be a little clearer I have a system whereby I have a protein interacting
with SWCNT. I used the NAMD energy plugin to calculate interaction energy.
When setting up NAMD energy I specified an XSC file which was the latest
one in the trajectory working files. NAMD then uses this as a reference to
predict subsequent PBC coordinates. If I do not specify that XSC, I get a
interaction energy curve with a lot of gaps (see powerpoint attached).

Is there any way I can get NAMD to give me this XST file?

Best,
Aryan Vahedi
Morgan State University

Powerpoint Link:
https://drive.google.com/file/d/0B0hL_QDtohLAS3pIeHlhS2xpSEE/view?usp=sharing