NAMD Simulation error

From: Anirban Ghosh (
Date: Wed Nov 12 2008 - 22:41:07 CST


I am running a simulation of a residue based CG model of 856 CG beads in
NAMD. I am running it using implicit solvent condition without PBC and
PME. After 5000 steps of minimization the system ran for 550000 steps and
gave a error:
LDB: LOAD: AVG 0.110926 MAX 0.150218 MSGS: TOTAL 38 MAXC 7 MAXP 7 None
LDB: LOAD: AVG 0.110926 MAX 0.112707 MSGS: TOTAL 38 MAXC 7 MAXP 7
ERROR: Atom 744 velocity is 684.102 -844.858 588.241 (limit is 1000)
ERROR: Atom 750 velocity is -555.261 769.693 -387.632 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.
WallClock: 929.760376 CPUTime: 643.129211 Memory: 7608 kB

In the error the atom velocities did not cross 1000 (which is shown to be
the limit) but still it terminated. I am getting the same error but at a
very early stage if I use PBC and PME. I have tried increasing the box
size also and now without PBC, but every time I am getting this error. The
configuration script is attached. Please suggest a solution. Thanks


Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:29 CST