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