On Thu, Oct 14, 2004, xiaowei li wrote:
> I am trying to perform normal mode analysis after energy
> minimization using SANDER. But I met following problem:
>
>
> ***************** ***************** *****************
> step = 0
> F = -0.285807E+03 GRDMAX = 0.192852E+01 GNORM = 0.431100E+00
> E-NONB E-ELE E-HBOND E-BOND
> -0.37231E+03 -0.32143E+03 0.00000E+00 0.10605E+02
> E-ANGLE E-DIHED E-NB14 E-EEL14
> 0.80886E+02 0.37009E+03 0.14107E+03 -0.19473E+03
> E-POL E-3BOD
> 0.00000E+00 0.00000E+00
> Root-mean-square gradient of input coords is 0.431099703381535
> This is greater than the requested maximum: 1.00000000000000D-004
....
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 342250 -4.1562E+02 8.9638E-06 6.1266E-05 C3' 209
>
> BOND = 10.6048 ANGLE = 80.8864 DIHED = 370.0898
> VDWAALS = -372.3060 EEL = -321.4318 HBOND = 0.0000
> 1-4 VDW = 141.0750 1-4 EEL = -324.5417 RESTRAINT = 0.0000
I'm hoping(!) that, before asking for help, you examined the numbers and
noted that everything is the same except for the 1-4 electrostatics. That
would then guide you to looking for things that affect this energy. You would
probably then discover that the default value for scee is 1.2 in sander, and
is 2.0 in nmode (for pretty dumb historical reasons.) Therefore, you need to
set scee=1.2 in nmode.
....good luck....dac
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Received on Fri Oct 15 2004 - 00:53:00 PDT
