Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this.
Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: > 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 > > [email protected]_ > Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected] http://folding.bmc.uu.se -- 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
