Dear GROMACS users, I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I am getting a Total Energy between -1.2 to 0.6 KJ/mol (already normalizaed, Total energy/#molecules). I checked the potential energy at the end of minimization and this was around -65 kJ/mol. Then, I observed that during NVT equilibration my potential energy decreased to a value around -33 kJ/mol with a kinetic energy also around the same value (33 kJ/mol), and that's why my final total energies and, therefore, enthalpies are giving values around 0. I ran also simulations with water, isopropanol, and acetonitrile and I am getting values of -52, -206, and-48, which seem reasonable to me. My paremeters have been already discussed in a previous mail (please see acetonitrile with CHARMM ff), and they seem to be right to be used with CHARMM ff. I am using version 2016.3 (I did the sa me in 5.1.2), sd integrator, Berendsen barostat for equilibration and P-R for MD production. Any ideas of what should I look for or what can I be doing wrong?
Thank you very much!!!, Sonia Aguilera PhD student ENSCM -- 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.
