On 3/20/18 2:40 PM, Alex wrote:
Dear all, The potential energy of my system after two minimization steps (with and without constrained) is converging well, however, it is still positive around 1000 kj/mol ! I think it is not a good sign for my system, but, what could be the reason and how I can overcome the issue? The system generated via "gmx insert-molecules" contains 1000 molecules of "C21H28O4".
Look at the individual values of internal (bonded) terms and nonbonded terms. Likely the intermolecular interactions are fairly weak, and the potential energy of the system is dominated by internal terms, which are by definition positive.
Second question; To calculate the RDF between pair of atoms, let's say A and B, I was wondering if those two atoms should be differentiated in index.ndx file from beginning before invoking the gmx gromps?(similar to energygrps) or one can does the simulation without index.ndx and still possible to calculate the RDF between those two atoms?
There is no need for anything like energygrps. If you want to exclude the intramolecular contribution to the RDF (if relevant), you have to increase nrexcl in the topology and generate a new .tpr, otherwise everything is controlled by index groups.
-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.
