during a 200 ns simulation of a protein complex in water in the 150th nanosecond they fall apart. I have retrieved the complex from PDB. I wonder whether someone can help me with that should I continue the simulation or should I change my force field or...
Best Regards
The first thing I would do is to check the log file from the production run. What message you get there determines the next action. Documentation about this error may also help:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Hi Nesa,
You should check the interaction in the interface of your complex. Are there any specific interaction like hydrogen bonding, salt bridge or pi-pi interaction ? If not, your result may make sense.
Hi, It has all the interactions you mentioned above but still they fall apart.
Dear Nesa,
Does this protein-protein complex structure (is taken for simulation) from rcsb?
or you have prepared the protein-protein complex ?
If you have docked protein-protein complex than,
By using editconf convert the .gro to .pdb and visualize after removing water molecule. I feel kindly visualize the structure not only after minimization but also before running simulation you will get your answer.
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