From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 22 2007 - 19:24:26 CDT
NAMD will die if you're missing parameters, so that isn't the issue.
Could you check your starting coordinates and make sure they look
reasonable? Most often this sort of problem comes from a very
unreasonable starting conformation, such as two atoms with identical
coordinates...
Peter
namd vmd wrote:
> 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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