Hi Peter, Thank you for the swift reply. Here are some details about your answers. I hope the problem will appear more clear with them.
> Increase/decrease by how much? Is it converged? The results completely diverge, that is the problem. The interactions we are observing through the simulations are in opposition: attraction with high dump rates (25000 steps) or repulsion with low dump rates (2500 steps), hence the change in box size. This is why we are confused about these simulations. > Don't do this (http://www.gromacs.org/Documentation/Terminology/ Thermostats) We use two coupling groups: one for the sugar molecules and the solvent (water), and the one for a macromolecule interacting with the sugar. > Simulations perfomed by Gromacs are not binary reproducible, so you will > (never) get exactly the same result twice starting from the same point. > This is inherent in how the simulation is performed. > http://www.gromacs.org/Documentation/Terminology/Reproducibility > This is why sampling is so important, to show that the fluctuations you > see average out and are not depending on stochastic errors or the > starting conformation. Similar answer than in the first point: the problem are not the fluctuations between measurements leading to the same average result, but the complete divergence between the behiavors at low and high dump rates. Best regards, Vivien -- Dr. Vivien WALTER ------------------------------------------------------------ Institut Charles Sadron 23, Rue du Loess BP 84047 67034 STRASBOURG CEDEX 2, France ------------------------------------------------------------ tel: +33(0)388 414 113 fax: +33(0)388 414 099 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
