[gmx-users] Effect of refcoord_scaling
chris.neale at mail.utoronto.ca
Wed Sep 5 16:46:04 CEST 2012
refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know what exactly you are doing with position restraints
in order to provide the most useful advice.
Nevertheless, you ran 2 simulations and got different results. It is not prudent to
assign the difference to refcoord_scaling at this point. To test this yourself, please
repeat each simulation (ideally at least 3 simulations for each case with and
I am not sure what happens with pressure coupling but using refcoord_scaling=no
(the default). The manual says:
"Note that with this option the virial and pressure will depend on the absolute
positions of the reference coordinates."
I interpret this to mean that you will get the wrong pressure, and my hunch is that
this would not significantly affect the stability of a DNA-protein complex, but you'll need
to test that out yourself.
A final note is that you should be sure to use the exact same conformation to start your
runs both with and without refcoord_scaling=com. Either start with this conformation and
redo the minimization, solvation, etc for each replica or pick one of your minimized initial
conformations to start all of your production runs. This is important so that you avoid
the situation in which some stochastic event in your system setup (pre production runs)
actually lead to the difference.
-- original message --
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
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
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
Thank you very much for your help,
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