AW: MD crashes at 300K after warm up MD

From: Norman Geist (
Date: Wed Mar 20 2013 - 02:36:02 CDT

Hi Patricia,


If I understood correctly, you are using the coor file from the 315K run and
no vel file, but set the initial temperature to 300K. The only reason I can
imagine, is the fact, that the 315K are still represented due the
coordinates. There’s a phenomenon where you can remove all velocities to a
system, so run it from 0K, and it will quickly get back to the half of the
temperature represented in the initial coordinates. This is because, so I
think, the higher temperature cause faster atoms and so increase the range
of fluctuation of bonds and angles. This increases the potential energy
which unloads when you just removed the velocities.


So if all the above is right, using a short temperature controlled run to
equilibrate your system to 300K should work. Or is there a special reason
why you want to do it in that way?


Norman Geist.


Von: [] Im Auftrag
von Patricia Campbell
Gesendet: Dienstag, 19. März 2013 19:30
Betreff: namd-l: MD crashes at 300K after warm up MD




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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