[gmx-users] Andersen thermostat

[Justin A. Lemkul]

Sai Pooja wrote:
> Hi,
> 
> I want to use the Andersen Thermostat (not v-rescale). But I get an 
> error when I try to use it. My mdp file is as below:
> 

My guess is that the error stems from the fact that the Andersen thermostat has 
not been implemented in Gromacs.  Manual section 7.3.14.

-Justin

> title                    =NPT simulation for a 2D WCA system
> cpp                      =/lib/cpp
> 
> ; RUN CONTROL PARAMETERS
> integrator               = md
> dt                       = 0.0005
> nsteps                   = 400
> 
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 50  ; No output, except for last frame 
> (coordinates)
> nstvout                  = 0    ; No output, except for last frame 
> (velocities)
> nstfout                  = 0    ; No output, except for last frame (forces)
> nstlog                   = 100   ; Write every nth step to the log
> nstenergy                = 100     ; Write energies at every n step
> nstxtcout                = 0     ; Do not write a compressed tr
> 
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 10
> ns-type                  = Grid
> pbc                      = xyz
> rlist                    = 0.9
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = Cut-off
> rcoulomb                 = 1.1225
> vdw-type                 = Cut-off
> rvdw                     = 1.1225
> 
> ; Temperature coupling
> tcoupl                   = Andersen
> tc-grps                  = ARAR
> tau_t                    = 0.1
> ref_t                    = 120.2717
> andersen_seed            =-1
> 
> ; Pressure coupling
> pcoupl                   = Berendsen
> pcoupltype               = semiisotropic
> tau-p                    = 0.20 0.20
> compressibility          = 1e-5  0   ;Dont know
> ref-p                    = 50 0
> 
> 
> ;Generate velocities for startup run
> gen_vel                  =yes
> gen_temp                 =120.2717
> gen_seed                 =-1
> 
> ;Constraints
> constraints             = all-bonds
> constraint_algorithm    = LINCS
> lincs_order             = 4
> lincs_iter              = 1   
> lincs_warnangle         = 90
> ;unconstrained_start    = no
> ;shake_tol              = 0.0001
> 
> 
> 
> Any idea why this would not work?
> 
> Pooja
> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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