Hi Chris,
thank you for your answer.
Let me comment on some of your hints.
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.
Yup, that's right, I forgot to mention this (sorry). I am running simulations
of a complex of a protein with a DNA double helix. In test simulations, I found
that the DNA distorts almost immediately if it's free (it looks like the double
helix will un-wind and bend, resulting in a lot of mdrun warnings and finally
abort because of large movement, even at 0.5fs timestep) and this movement
affects the DNA-protein interactions.
To avoid the distortion, I thought I can apply position restraints on the DNA
to keep it in place (more or less) to get a better picture of the interaction.
Is there another way to do this?
And what came to my mind when I considered this, if I apply position restraints to a
molecule to kind of "fix it" in a NpT simulation, should I include or exclude
it in the tc_grps (or maybe include at T=0)?
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).
That sounds reasonable and I think I ought to do this. Unfortunatly the
simulations are quite expensive and I have a (quite hard) deadline next week
when I have to submit my diploma thesis. So, I think I will not be able to
repeat these simulations before. Even if I start them now, they will not be
finished (even if they start soon which, too, is unlikely). Still, I can do
this afterwards.
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.
This is exactly the point why I wanted to ask if somebody has experiences with
this issue and can tell us what this combination of parameters can cause in a
simulation.
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.
Okay. What I did was to start with the same structure and then apply a
several-step protocol similar to the tutorials to it: EM in vacuo, add solvent
and EM, add ions (only to neutralize it, no excess salt concentration) and EM,
MD with entire system position-restrained, MD in NVT-ensemble for equilibration
of temperature, MD in NpT-ensemble for equilibration of pressure and then,
finally, production MD. This whole protocol was carried out for both of my
simulation, so the initial positions of the ions are quite different and maybe
this plays a role, too. Apart from this (and the velocities of the particles),
the setup is identical.
The proper step to "jump in" when repeating the simulations seems to be before
NpT-equilibration.
Please, if you see some obvious (or not so obvious) mistake in what I'm doing,
tell me. One question that also could not be resolved after reading the
tutorials was if it is good/necessary or rather a bad idea to continue with the
old velocities in the equilibration steps. Some tutorials do, others don't...
Sorry if there are some rather simple questions, but unfortunately I don't have
a supervisor who knows GROMACS and who could tell me what to do or answer my
questions. In addition, I did not have much time to get used to all this as in
the beginning, the project was meant to use MC simulations instead of MD what
took me a rather long time to implement and to find out that this does not work
well.
But still, I have some results. I want to understand them well and make sure
next time, I will do less mistakes...
Thanks for your help,
Matthias
Chris.
-- 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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