Project

General

Profile

Bug #3073

Total potential energy goes crazy, but I don't know why this happens.

Added by Siyoung Kim about 1 month ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Hi, the total potential energy goes +nan as follows:

@ s0 legend "Potential"
0.000000 -6837739.000000
2.000000 -6792606.000000
4.000000 -6799583.000000
6.000000 -6803802.500000
8.000000 179819456286476482591022087405568.000000

or in the slurm file, the error is shown as follows:
Fatal error:
Step 5000: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are 11004.6 and -1.05819e+06,
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.

However, once checking upon each potential from the .edr file such as Bond, U-B, Dihedrals, LJ-14, Coulomb-14, LJ-(SR), Coulomb-(SR) and Coul.-recip., everything is fine.
I am using Gromacs 2019.3 and running simulations using a GPU node. I attached .tpr and .edr file.
Thanks!

Best,
Siyoung

md.edr (3.91 KB) md.edr Siyoung Kim, 09/04/2019 07:24 PM
md.tpr (23.4 MB) md.tpr Siyoung Kim, 09/04/2019 07:24 PM

Also available in: Atom PDF