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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 12 13:17:35 CET 2009

Siavoush Dastmalchi wrote:
> 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:

tpbconv allows you to create subsets of .tpr files, so you should also 
use trjconv to make a matching subset from your .trr files and then use 
mdrun -rerun.

> ******************************
> 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.
> ******************************

This does not look like you are doing a rerun. LINCS should not be 
invoked, IMO.


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