Dear Gromacs users, I am a little new fellow in this community, and many things still I don't know.
I am trying to parametrize a coarse-grained FF for polymer simulations, without solvent. A collegue of mine advised me, just to be sure, to check for possible energy leak artefacts. To do that he told me that I should run a simulation with no thermal coupling and check the energy conservation. He told me that in such case, in a well-behaved system, "dE/E<10-4, 10-5" (where dE is the RMSD?). By playing with that indeed I found that, as expected, using pme-switch and shift for Coulombd and VdW respectively helps a lot (with respect to cut-offs), but even increasing LINCS, decreasing neighbour search time etc. my ratio doesn't go below 2E-3. I wonder however if there are also possibly poor minimization effects in that -it seems that it minimizes correctly, but... My problem however is that apart from that informal advice I can find very little practical on the subject. The only clear thing I can find on the net is a Van der Spoel students tutorial which says: https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html#mozTocId961213 "Conservation of energy can be monitored by checking the ratio of the fluctuations in Total energy and the Kinetic Energy. For a well behaved system the ratio R: R = Δ Etot/Δ Ekin should be less than 0.05." but it doesn't specify, as far as I can see, the conditions in which this is a good ratio (solvent, no solvent, which thermostat, etc.). Has anyone advices for bibliography or some general practical wisdom on this problem? Thanks a lot, Massimo -- 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/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/mailing_lists/users.php
