Jocley Araujo wrote:
Hello
I had a problem with mdrun while trying to run trajectories for protein
ligand complexes. I`ve already done successful calculations with 60
complexes, unfortunately 4 complexes gave the following error. The
entire output is too big to copy, so I have only copied the error part.
But lots of numbers appear before this error.
Program mdrun, VERSION 4.0.4
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (1522)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
-------------------------------------------------------
These ligands all have in common the nitrile group linked to an aromatic
ring. I am using the gromos 53a6 forcefield. The minimization step ran
normally for these complexes, so I only had problems when I tried to run
the md simulations. I have alreay tryed some of the solutions given by
the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has
something to do with the nitrile group. Has anyone had any problem like
this before?
I would like some help on the matter
You need to define a virtual site.
If you have C1-C2#N3 you want to make a bond (constraint) between 1 and
3, and define 2 as a vsite (check manual).
Jocley
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