From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Sep 27 2016 - 00:14:49 CDT
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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