AMBER Archive (2009)

Subject: [AMBER] long polymer chain and image command in ptraj

From: iccy liu (
Date: Thu Apr 02 2009 - 14:11:26 CDT

Hi, all,

I met a challenge in my simulation and would like to hear experts' opinions about that. I started my simulation with an extended long polymer chain, solvated in water. my solvent box is a rectangle prism with one dimension much longer than other two. I set up periodic boundary condition in my simulation. During my simulation, I observed that one end of my polymer chain (sometimes two ends) moved out of the solvent box and the polymer also turned to fold together. I assum it is not a problem since the periodic boundary condition is actived. However I had a hard time to analysing my trajectroy. I tried to use image command and couldn't get a reasonable trajectory. Also because of my polymer folded, it is impossible to be fit in the original rectangle prism anymore. I wonder did anyone meet similar problems before? Any input will be highly appreciated.

Thanks in advance,

Iccy Liu

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