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. 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. 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. Thanks in advance, Saber -- 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
