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.
Mark
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