[gmx-users] using rerun to extract energies for protein from trr file

Siavoush Dastmalchi Dastmalchi.s at tbzmed.ac.ir
Mon Jan 12 09:20:29 CET 2009

Dear list,

I am trying to extract energy profile for a protein molecule using rerun program from trajectory obtained by MD of protein solvated in a water box. I have created index file and reedited the original mdp file (removed the SOLs from it) to get a new tpr file using grompp. I have extracted a coordinate file and also generated top file for this coordinate file. When I run the mdrun using -rerun option, it fails and gives the following error message:


Program mdrun_d, VERSION 3.3.1
Source code file: clincs.c, line: 559

Fatal error:
Too many LINCS warnings (11741) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations.
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file, but normally it is better to fix the problem.

I will appreciate if you could kindly let me know what I am doing wrong.

Cheers, Siavoush

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