Hi, Although your preparations seem sensible and a good starting point for stable simulations, I suspect that the source of the error is in your mdp-file or in how you constructed your simulation box. I've simulated complexes like yours for hundreds of nanoseconds without problems. Could you provide your mdp-file for us to look at?
Best, Erik 6 sep 2012 kl. 00.31 skrev Matthias Ernst: > 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 > > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html -- 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
