Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan"

From: namd vmd (namd.vmd_at_gmail.com)
Date: Thu Mar 22 2007 - 07:55:00 CDT

The molecule is gamma-amino butyric acid.

PARAMETERS: The molecule has standard atom types, and NAMD did not complain
of any missing parameters, so I did not add any parameters.

TOPOLOGY: Hereis the topology (also attached with this email, in case of
formatting issues). The topology was built by using groups from the lysine
and the glutamate side chains.

RESI BUTY 0.00

GROUP
ATOM CE CT2 0.21 ! HZ2
ATOM HE1 HA 0.05 ! |
ATOM HE2 HA 0.05 ! (+) HZ1---NZ---HZ3
ATOM NZ NH3 -0.30 ! |
ATOM HZ1 HC 0.33 ! |
ATOM HZ2 HC 0.33 ! HE1---CE---HE2
ATOM HZ3 HC 0.33 ! |
GROUP ! |
ATOM CD CT2 -0.18 ! HD2---CD---HD1
ATOM HD1 HA 0.09 ! |
ATOM HD2 HA 0.09 ! |
GROUP ! |
ATOM CG CT2 -0.28 ! HG1---CG---HG2
ATOM HG1 HA 0.09 ! |
ATOM HG2 HA 0.09 ! CB
ATOM CB CC 0.62 ! // \
ATOM OE1 OC -0.76 ! OE1 OE2 (-)
ATOM OE2 OC -0.76

BOND OE2 CB CG CB CD CG CE CD NZ CE
BOND CG HG1 CG HG2 CD HD1 CD HD2 CE HE1 CE HE2
BOND NZ HZ1 NZ HZ2 NZ HZ3
DOUBLE OE1 CB

On 3/21/07, namd vmd <namd.vmd_at_gmail.com> 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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