From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Mar 21 2007 - 13:54:47 CDT
May be you should start by sending the topology/parameter files for your
custom molecule.
namd vmd escribió:
> 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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