I am trying to run a simulation of single Na ion in implicit solvent(water), with OPLSAA FF in gromacs 4.5.7. After running the simulation and viewing the .log file I find that the initial temperature is set to 0 K even though I have mentioned a ref_t as 300 K. Why does this happen? Any help is much appreciated
Nichith ------------ .mdp file : integrator = sd nsteps = 500000 dt = 0.002 implicit_solvent = GBSA gb_algorithm = Still gb_epsilon_solvent = 80 pbc = no nstlist = 0 ns_type = simple rlist = 0 rgbradii = 0 coulombtype = Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 1 ref_t = 300 ;energygrps = Ion_chain_A Ion_chain_B gen_vel = yes gen_temp = 300 ld_seed = -1 gen_seed = -1 nstxout = 100 nstvout = 100 nstxtcout = 100 nstenergy = 100 part of the .log file after mdrun is --------- Using accelerated all-vs-all kernels. Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1e+18 Coulomb: 1e+18 LJ: 1e+18 System total charge: 1.000 Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest There are: 1 Atoms *Initial temperature: 0 K* Started mdrun on node 0 Wed Feb 19 02:03:12 2014 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) GB Polarization Nonpolar Sol. LJ (SR) Coulomb (SR) Potential -3.84741e+02 2.79270e+00 0.00000e+00 0.00000e+00 -3.81949e+02 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 -3.81949e+02 0.00000e+00 0.00000e+00 Step Time Lambda 100 0.20000 0.00000 Energies (kJ/mol) GB Polarization Nonpolar Sol. LJ (SR) Coulomb (SR) Potential -3.84741e+02 2.79270e+00 0.00000e+00 0.00000e+00 -3.81949e+02 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 -3.81949e+02 0.00000e+00 0.00000e+00 -- View this message in context: http://gromacs.5086.x6.nabble.com/Implicit-solvation-Initial-temperature-changes-to-0-K-tp5014609.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.