[gmx-users] stochastic thermostat

[Dmitry Nerukh]

Dear gromacs developers,

 

Can you, please, describe the steps for running a normal molecular dynamics
with a stochastic thermostat?  I have a very simple system - just 2 waters
in vacuum.  I've tried setting the integrator to 'sd' and 'tau_t' to 0.  The
integration failed.  Is it possible to have a stochastic dynamics with the
velocity friction term set to 0?

 

Thanks,

Dmitry.

 

constraints         =  all-bonds

integrator          =  sd

dt                  =  0.002   ; ps !

nsteps              =  400000         ; total 800 ps.

nstcomm             =  -1

nstxout             =  1

nstvout             =  1

nstfout             =  0

nstlog              =  10

nstenergy           =  10

nstlist             =  10

ns_type             =  grid

rlist               =  1.0

rcoulomb            =  1.0

rvdw                =  1.0

; periodic boundary condition

pbc                 =  no

; Berendsen temperature coupling is on in two groups

Tcoupl              =  berendsen

tc_grps                 =      SOL

tau_t               =  0

ref_t               =  300

; Energy monitoring

energygrps          =  SOL

; Isotropic pressure coupling is now off

Pcoupl              =  no

Pcoupltype          =  isotropic

tau_p               =  0.5

compressibility     =  4.5e-5

ref_p               =  1.0

; Generate velocites is on at 300 K.

gen_vel             =  yes

gen_temp            =  300.0

gen_seed            =  10007

 

 

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