From: Radak, Brian K (bradak_at_anl.gov)
Date: Tue Sep 27 2016 - 10:50:33 CDT
The "jumping" you see is a reassignment of the primary image based on the molecule passing through a periodic barrier. The "explosion" of water molecules is from diffusion of water and the molecules not being reassigned to the primary image.
What behavior are you looking for? It sounds like you want a freely diffusing protein molecule with water staying in the primary image (wrapWater on). However, I don't think you can both not wrap the protein and wrap water around it, because namd cannot know what the rules are for wrapping around a secondary image. You might be able to visualize this after the fact in VMD by turning on PBC images in the representation, but I don't think this change will transfer to your analysis script.
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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of sunyeping [sunyeping_at_aliyun.com]
Sent: Tuesday, September 27, 2016 12:14 AM
Subject: namd-l: Wrapall on or off?
When I set the namd paramter "wrapall" to "on" and do the simulation, in the resulting trajectories I sometimes can find part of the protein molecule jumps to the neighbouring periodical cell. After I use "pbc unwrap -all" command on the trajectory in VMD, the jumping part returns to its original site, but the water molecules seem to explode as individual molecules diffuse. I don't want the jumping behavior no the water molecules explosion because both of them cause difficulty for my analysis. So should I set the "wrapall" to "on" or ""off"? Or is there any other way to solve the problem?
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