From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Sat Apr 23 2016 - 09:30:08 CDT
I ran NVT simulation of a nano-tubes in addition to a dimer solvated in water. In the namd conf fileI turned on the wrapAll and wrapWater options. I saw that the nano-tube and dimer were somuch moving around and going out of the simulation box frequently during the simulation. Since I already turnedon the wrap options then sometimes either nano-tube or dimer jump from one side to the other sideof simulation box, depending on which one catching the side wall, not suitable for doing somecalculations. I then decided to unwrap the nano-tube (resname CNT) and dimer (resname ARG)by following command in vmd:
pbc unwrap -sel "resname CNT or resname ARG" -all
Doing so I calculated the total energy of the wrapped and unwrapped trajectories using namd energyplugin. I expected they show the same plot of total energy versus time, but they show slightly different plots.
Can anyone help on this? In addition to this I don't have a clear understanding of what wrapping optiondoes in namd or vmd as I see sometimes nano-tube or dimer traverses the cell side (one part pass the sideand one part still in the box) but it isn't wrapped and sometimes it is in the similar situations and it would be wrapped..Don't know exactly what it does.. Can anyone introduce me some reference or tutorial to understand more?
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