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?
Something is physically unrealistic about your system, leading to LINCS
crashing. Where did you get your parameters for the nitrile group? If this is
the common thread for the systems that crash, you can bet that whatever
parameters you are using are not reliable.
-Justin
I would like some help on the matter
Jocley
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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