VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Mon Nov 09 2015 - 04:09:48 CST

This is NAMD related question, VMD plot is only a plotting utility with
hardcoded column headers.
http://www.ks.uiuc.edu/Research/namd/2.10/ug/node12.html#1413
Pawel

W dniu 09.11.2015 o 09:22, sunyeping pisze:
>
> Dear all,
>
> I don't understand the definitions of some of the items listed in VMD
> plugin NAMD Plot, and I can not find them anywhere. Could someone
> explain those? For example, what is difference between "TOTAL",
> “TOTAL2" and "POTENTIAL"? If I want to use the system energy for
> further calculation, say, accelerated MD, which one should I take?
> Besides, what do the "BOUNDRARY", "MISC" and "KINETIC" mean? What
> is difference between "TEMP" and "TEMPAVG"? What is the difference
> between "PRESSURE", "GPRESSURE", "PRESSAVG" and "GRESSAVG"? And does
> the "VOLUME" mean the volume of the water box?
> I am using VMD-1.9.2, and the log file was produed
> from NAMD_CVS-2015-09-29_Linux-x86_64-multicore-CUDA. Are the items
> listed by the NAMD Plot plugin in different versions of VMD different?
> Or do they just change with the log file produced by NAMD of different
> version?
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>