[gmx-users] Effect of refcoord_scaling

Christopher Neale chris.neale at mail.utoronto.ca
Wed Sep 5 22:40:34 CEST 2012

As a side note: I would be very interested to know what type of artefacts one might expect when using refcoord_scaling=no with pressure coupling. I have no doubt that the description in the manual is accurate, but it is also kind of cryptic to those of us who don't already understand it.

Thank you,

-- original message --

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 
without refcoord_scaling).

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 
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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