[gmx-users] Effect of refcoord_scaling

Matthias Ernst Matthias.Ernst2 at student.kit.edu
Tue Sep 4 18:59:44 CEST 2012

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

More information about the gromacs.org_gmx-users mailing list