I second everything that Justin Lemkul wrote. This recent paper (C. A. Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012)) have a few weak points in my opinion, but demonstrate the artifacts that arise from freezing the DNA.
Best, Erik 9 nov 2012 kl. 20.42 skrev Justin Lemkul: > > > On 11/9/12 9:02 AM, saber naderi wrote: >> Dear Gromacs Users, >> >> I would like to study structure of a positively charged protein in the >> vicinity of DNA. To do this, I want to perform replica exchange molecular >> dynamics simulations in which DNA is frozen and only the protein moves. >> This way I can efficiently obtain the free energy landscape of the protein >> close to [frozen] DNA. >> >> The reason why I keep the DNA frozen is that this may reduce the >> computational cost in two ways: >> 1. DNA atom coordinates are not updated. > > Frozen groups do not improve performance. > >> 2. Maybe I can have a smaller simulation box (and less number of water >> molecules), because in principle I can exclude DNA-DNA interactions via >> energygrp_excl. >> > > This is also not true, as there are protein-DNA and protein-water > interactions that cannot be ignored. > >> so, I would like to ask you if you think this is a reasonable approach? >> What could go wrong in such simulations? Any input would be appreciated. >> > > Are you sure that there is no potential for the protein to induce any > structural change in the DNA? If you freeze the DNA, you assume that no > remodeling occurs. This assumption could impact the calculated free energy > of binding. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * 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 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
