[gmx-users] change simulation temperature

[Mark Abraham]

On 29/02/12, "bo.shuang" <bs16 at rice.edu> wrote:

> Hi, all,
> 
> I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I am thinking if I need to change tau_t also, since diffusivity constant is also related to temperature. Am I right?
> 
> Here is my mdp file:
> title        = OPLS Lysozyme NVT equilibration  
> ;define        = -DPOSRES    ; position restrain the protein 
> ; Run parameters 
> integrator    = bd        ; leap-frog integrator 

 
By their nature, Browning and stochastic dynamics do not work with temperature coupling algorithms. IIRC gen_temp + gen_vel should have an effect on the initial conditions.
 
Mark 
 

> 
> 
> nsteps        = 500000    ; 2 * 500000 = 1000 ps 
> dt        = 0.002        ; 2 fs 
> ; Output control 
> nstxout        = 100        ; save coordinates every 0.2 ps 
> nstvout        = 100        ; save velocities every 0.2 ps 
> nstenergy    = 100        ; save energies every 0.2 ps 
> nstlog        = 100        ; update log file every 0.2 ps 
> ; Bond parameters 
> continuation    = yes        ; first dynamics run 
> constraint_algorithm = lincs    ; holonomic constraints  
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) constrained 
> lincs_iter    = 1        ; accuracy of LINCS 
> lincs_order    = 4        ; also related to accuracy 
> ; Neighborsearching 
> ns_type        = grid        ; search neighboring grid cells 
> nstlist        = 5        ; 10 fs 
> rlist        = 1.0        ; short-range neighborlist cutoff (in nm) 
> rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm) 
> rvdw        = 1.0        ; short-range van der Waals cutoff (in nm) 
> ; Electrostatics 
> coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics 
> pme_order    = 4        ; cubic interpolation 
> fourierspacing    = 0.16        ; grid spacing for FFT 
> ; Temperature coupling is on 
> tcoupl        = V-rescale    ; modified Berendsen thermostat 
> tc-grps        = system    ; two coupling groups - more accurate 
> tau_t        = 0.01        ; time constant, in ps 
> ref_t        = 400         ; reference temperature, one for each group, in K 
> ; Pressure coupling is off 
> pcoupl        = no         ; no pressure coupling in NVT 
> ; Periodic boundary conditions 
> pbc        = xyz        ; 3-D PBC 
> ; Dispersion correction 
> DispCorr    = EnerPres    ; account for cut-off vdW scheme 
> ; Velocity generation 
> gen_vel        = yes        ; assign velocities from Maxwell distribution    changed 
> gen_temp    = 400        ; temperature for Maxwell distribution 
> gen_seed    = 100        ; generate a random seed 
> ld_seed=-1 
> 
> 
> Thank you!
> 
> Bo
> 
> 

 
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