starwingc / peptoid_24summer

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13AC1-6-A error with EM step #8

Closed starwingc closed 3 months ago

starwingc commented 3 months ago

All the file are in .../peptoid_24summer/peptoid/13AC1-6-A/GAFF/neutral/gaff1

The initial gro file looks of 13AC1-6-A looks like :

image

and when I try to perform the em, the error outputs is

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        50000

-------------------------------------------------------
Program:     gmx mdrun, version 2020.5
Source file: src/gromacs/mdlib/sim_util.cpp (line 465)

Fatal error:
Step 0: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are nan and inf, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I found there are some inf under the 13AC1-6-A.itp, I think I should manually fix them but I don't know how.

[ pairs_nb ]
         6          8      1  -0.567900       -inf             nan             nan
         6         16      1  -0.567900  -0.047753     3.17980e-01     3.17088e-01
         5          9      1   0.597200  -0.128587     1.00000e-01     0.00000e+00
         5         15      1   0.597200  -0.128587     1.00000e-01     0.00000e+00
         5         17      1   0.597200   0.487330     1.00000e-01     0.00000e+00
         2          8      1  -0.366200  -0.028920             nan             nan
starwingc commented 3 months ago

The issue is solved by change the [atomtypes] crazy mass, and calculate the epsilon factor by hand