From: namd vmd (namd.vmd_at_gmail.com)
Date: Wed Mar 21 2007 - 12:38:42 CDT
Hello NAMDers,
I ran a simulation of an amino acid with a lipid bilayer, and it ran
smoothly.
With the same bilayer, I ran a simulation with a different molecule instead
of the amino acid. The topology of this molecule is not available, and I
constructed it independently. NAMD did not complain about any missing
parameters, but the simulation explodes and I get the following lines
(repeated many times) when I try to minimize the system
======================================================
INITIAL STEP: 1e-300
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
The inital energy of the system (obtained by minimizing for 0 steps) is as
follows:
TCL: Minimizing for 0 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 22755.0144 99999999.9999 3645.5707
99999999.9999
-91809.4361 99999999.9999 0.0000 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000
99999999.9999 99999999.9999
========================================================
I am sure that the problem lies in the parameters, because the simulation
with the amino acid worked just fine. I also tried increasing the PME grid
resolution, the cutoffs, and the pair-list-dist, but nothing helped.
Can someone please explain what might have gone wrong. The energy of the
"angle" term above is infinite, so it might have to do with some missing
parameters ?
PS: I did not have to define any new atom types for my new molecule.
thank u
-Rose
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