On Wed, Jun 12, 2013 at 11:26 AM, C.M.Sampson <[email protected]> wrote:
> 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? > Many issues with md-vv have been fixed since 4.5.5. Please update and try again. > > 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? > I couldn't follow your equation above, but the most likely issue would be the use of some algorithm that reduces the number of degrees of freedom, e.g. rigid water/bonds. Mark -- 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
