From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Wed Jan 19 2011 - 10:17:45 CST
I'm simulating a protein where its CYS is deprotonated and bound to Zn2+.
I did some modification to the topology file. After the modification, CYS'
charge is -0.8 while Zn2+ has a charge of 1.2.
When I evaluate my system charge with the command below:
set sel [atomselect top all]
eval vecadd [$sel get charge]
The charge of my sys tem is -0.39999932795763016.
I wana run my system in PME. So, is there any way I can neutralize my
system? Or it's ok for me to proceed to the simulation without neutralizing
All suggestion are welcomed.
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