I want to run an MD simulation for Protein-ligand complex and following Gromacs tutorial of Justin Lemkul Department of Biochemistry, Virginia Tech. I have successfully simulation until the and of the steps. in this case i try to do the similarity simulation with more complex structure that consist of Protein-DNA-and ligan. overall i succesfully generate the topology until em (minimization energy) steps, the graph intepretation looking good,
when write this command i,e mdrun -deffnm nvt some problems were happen following this warning below:
WARNING: Listed nonbonded interaction between particles 3921 and 3945
at distance 3.222 which is larger than the table limit 2.433 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Segmentation fault (core dumped)
what the solution for this problem? thank you
Any number of things could be wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for tips and diagnostic procedures.
If you're following my tutorial and using GROMOS, there are better nucleic acid force fields out there. If you're following my tutorial and *not* using GROMOS, then be sure you're using the appropriate .mdp settings and not just blindly applying the input files that are provided with the tutorial.
thank you Mr. Justin Lemkul for your email replay, and i do sorry for my directly email for you. i am new user for gromacs and a little problem makes me scared.
two days ago, Actually i solved my problem, that crash was caused by some side of the structure/protein complexes out of the box. Everything runs well when i justify the protein to the center.
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