Gmx-users,
I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit = 0 dt = 0.001 nsteps = 10000000 nstxout = 20000 nstvout = 20000 nstfout = 0 nstlog = 100000 nstenergy = 100000 nstxtcout = 20000 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist = 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r = 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t = 0.1 ref_t = 300 Pcoupl = no Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk
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