Dear Gromacs users,
I am currently working on Protein-DNA-complexes. They should be
simulated in NPT-ensemble.
I did the same simulation including previous minimization steps (in
vacuo, with solvent, with solvent and ions) and equilibration (system
position restrained, with theromstate, with barostate) twice with one
slight difference: in the second case, there was a GROMPP warning that
NPT (Berendsen-barostate) needs refcoord_scaling to avoid artifacts,
therefore I added "refcoord_scaling=com" to my mdp file.
The systems showed significantly different behaviour. In the first run
(without refcoord_scaling), the protein-DNA-complex was unstable and
some of the contacts between them broke. In the second run, the complex
remained stable.
As I do not have much experience with explicit solvent and ions MD
simulations, wondered if this difference can be caused by the lack of
reffcoord_scaling command.
The other guess would be that this comes due to an ion that drifts in
between the DNA and and the protein and therefore causes the distortion
of the protein.
Which do you think would be more likely? And which types of artifacts
can be caused by lack of refcoord_scaling and can they be seen or
detected easily?
Thank you very much for your help,
Matthias Ernst
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