[gmx-users] (Implicit solvation)Initial temperature changes to 0 K

[nichith]

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




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