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, Chris. -- 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. 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
