From: Alejandro Ortega (morza05_at_gmail.com)
Date: Tue Jul 08 2008 - 13:20:33 CDT
I'm having trouble when I run my simulation in NAMD. I have a simulation of
a water box, only. But when I run it namd tells me that simulation has
become unstable due to atoms going too fast.
I tried the command reinitvels but it doesn't work either. I think it has to
be with the bond energies but I don't know what am I doing wrong. It also
tells me that I have absolute/relatives imprecisions on the VDW table.
I tried to minimize energies in the program Chem 3D with the tool MM2, but
the program modifies the original PDB. What else can I do in order to
minimize the energies of my molecules?
Also, I noticed that the temperature doesn't seem to work on the
configuration file, if I give a value of 100K, the simulation behaves the
same as if I give a value of 500K,
In conclusion, how could I correct the atoms velocities and the values of
the VDW table? and does someone know why the temperature doesn't seem to
affect my simulation?
Any kind of help would be highly appreciated.
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