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Hello Jie-rong--
>
> Some error messages at the first begining of terminal window that I didn't
> notice last time:
> ############
> calcD_G: singular D matrix: { { nan } }
> H matrix: { { nan, nan, nan, 0, 0, 0 } }
> node level: 227
> number of children: 0
> atoms:
> 1228 GLY 76 C : { nan, nan, nan }
> 1229 GLY 76 OT1 : { nan, nan, nan }
> 1230 GLY 76 OT2 : { nan, nan, nan }
> ############
> Is this the second possibility you mentioned?
The NANs confirm that the gradient is the problem. You will need to
figure out which potential term is causing these by disabling terms one
by one.
>
> The pdb and psf files input are both:
> ############
> ATOM 1229 C GLY 76 127.034 0.640 -0.873 1.00 1.00
> ATOM 1230 OT1 GLY 76 127.291 -0.478 -1.288 1.00 1.00
> ATOM 1231 OT2 GLY 76 127.580 1.657 -1.268 1.00 1.00
> ############
> ############
> 1229 76 GLY C C 0.140000 12.0110 0
> 1230 76 GLY OT1 OC -0.570000 15.9990 0
> 1231 76 GLY OT2 OC -0.570000 15.9990 0
> ############
> The atom numbers are inconsistent with those indicated in error message, is
> it the problem?
>
no. Atom numbers differ between the C++ and Fortran code.
best regards--
Charles
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