[gmx-users] frezzing a bond : NPT and NVT simulations

Nilesh Dhumal ndhumal at andrew.cmu.edu
Sun Jul 25 17:42:49 CEST 2010


I am trying to freeze a bond (3.5 A) in my system.  I used the index file
to define group and I added this two lines in my .mdp file.

freezegrps         = PA NE
freezedim   = Y Y Y Y Y Y

I used g_dist to verify the distance between the freezing atoms. During
the NVT simulation the distace is around 3.449 A and its constant though
out the simulation. For NPT simulation the distance varies from 3.449 to
Can you tell why distance changes in NPT not in NVT.
How can I freeze a bond om NPT simulation?


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