MD crashes at 300K after warm up MD

From: Patricia Campbell (
Date: Tue Mar 19 2013 - 13:30:23 CDT


I am trying to run an MDFF package in VMD to run a NAMD simulation in
explicit solvent with several monomers of the same protein. After
minimization steps I warmed up the system to a point where TEMP and TEMPAVG
were both 315 K. This simulation ended there without any faults. I then
tried to run a simulation based on the trajectory of that simulation that
starts at 300 K and it crashes due to atomic velocity on the first step. I
have tried to increase the margin as well as pairlistdist and neither were

my cell values are:
CRYST1 220.067 184.388 211.949
and in my NAMD file:
cellBasisVector1 220.0570011138916 0 0
  cellBasisVector2 0 184.2920150756836 0
  cellBasisVector3 0 0 211.87700653076172
  cellOrigin -122.66092681884766 -216.130859375 -26.024154663085938

I want to take the last step and run a MD simulation at 300K for over
500000 steps. Thank you for your time.

Patricia Campbell

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