From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Wed Oct 03 2012 - 10:14:09 CDT
Dear Namd users,
I have ran several simulations in NPT ensemble and I did not wrap the molecules b/c I wanted to get smooth movement of the peptide (for making nice movies from the simulation results). Now I want to get some density distributions from some the system species but I have encounterd with the problem than I should wrap back the coordinated in order to get the distribution plots (I need exact box dimension for that purpose). However, since the simulation has been run in NPT, the size of the box changes and because I did not wrap the molecucles in the simulation the "measure minmax" can not give me the box dimension anymore!!!
Also in the standard namd output, I can see that the volume is reported but not the dimensions in x, y, z
can anyone please help? can I use these simulations to these density distributions??
looking forward to hearing something positive!!
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