[gmx-users] system blowing up

abhisek Mondal abhisek.mndl at gmail.com
Thu Dec 1 19:23:35 CET 2016


I'm constantly getting a strange error of system blow up during
equilibration procedure. I'm relatively new to gromacs, please help me to
get my things straight.

I have a ligand bound protein structure in solvated condition.
So, I was using:
gmx mdrun -v -deffnm em #for minimization

Upon successful completion, I try to equilibrate using:
gmx mdrun -deffnm npt

But this command is failing with a lot of LINCS errors.
Surprising thing is that, I'm running the same code in 2 clusters
simultaneously. In one cluster it is running fine but in other cluster it
is giving me LINCS error.

Can you please suggest what actually is going wrong.

Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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