Dear all, I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE simulations on ethane in 725 TIP3P water molecules. I used antechamber to parametrise my ethane.
I have 2 issues; Firstly the energy conservation of my simulations seems to get worse as I lower my timestep, here is an example .mdp file that I'm using: integrator = md-vv gen_vel = no nsteps = 1000000 dt = 0.001 nstlist = 10 rlist = 1.3 coulombtype = pme rcoulomb = 1.0 vdw-type = Shift rvdw = 1.0 tcoupl = no pcoupl = no nstenergy = 100 I found a link describing that it could be an issue with the precision and that Gromacs can be installed with double precision: http://www.gromacs.org/Documentation/Terminology/Conserving_Energy but is this the only way to ensure energy conservation? My second issue is with the calculation of the kinetic energy, I have 2183 atoms in my simulation box which means the kinetic energy should be (roughly) 0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) * 4.184(conversion from kcal/mol to kJ/mol) = 8163.97 however, when I look in my simulation the kinetic energy Gromacs outputs is 5498.20 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 5.95743e+00 1.96046e+01 4.71247e-01 5.73520e-01 3.92661e+00 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 5.12842e+03 -3.20604e+04 -2.67111e+03 -2.95726e+04 5.49820e+03 Total Energy Temperature Pressure (bar) -2.40744e+04 3.02575e+02 -1.82251e+03 By running in NVE I'm not using a thermostat and can't find any reason in the manual to scale the kinetic energy. Is there an a reason I'm missing as to why my kinetic energy seems lower than it should be? Best Wishes Chris -- 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
