From: Parisa Akhski (
Date: Sun Oct 31 2010 - 19:53:47 CDT

Dear VMD users,

I have two questions and would really appreciate if anyone could help me:
1. I have done a MD simulation in three restart jobs. I would like to first load all dcd files after each other to save
all trajectory files (dcd files) as one dcd file. Then, I want to unwrap the whole system. The problem is that I cannot use VMD on my PC (windows/ Ubuntu) to load more than 7000 frames while I have overal 100000 frames.
My guess is that I may be able to do this using super computers but, I don't know where I can find the commands for text mode VMD on Unix. Is there any document which can provide me with this information?
2. Since I have an idea of which frames I would like to study for now, I can only load those frames on my own PC.
But, I realized that to unwrap the system if I don't start from the first frame, the results of unrwap don't seem to be correct. I am wondering how unwrap works (I mean does it take the coordination of the system for the first frame and unwraps all system for the next frames with respect to the first one?) If so, I can only load the first frame and the ones I need to unwrap without the need to load the whole trajectory files.

Many thanks,