On 8/30/17 9:33 AM, Sergio Manzetti wrote:
Weird stuff, because the 1 simulation turned out well, even without POSRE. Can this POSRE be reliable, in terms of intercalation of molecules? In other words, does the energy that is imposed by POSRE really reflect the energy landscape of the bonds simulated in the remaining of the molecules in the box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then any intercalation study is really futile!
You're talking about both constraints and restraints here, and typically restraints are applied to non-H atoms and constraints involve bonds to H atoms. Restraints are biasing potentials to prevent motion. You'll have to explain what you're studying and why you think you need restraints (which are typically only used during equilibration). Restraints are artificial, so anything that comes out of a restrained simulation should be interpreted with care, because you could be completely preventing relevant dynamics. Binding of a molecule to a restrained target may be completely unphysical.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
