[gmx-users] change simulation temperature

[Justin A. Lemkul]

bo.shuang 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?
> 

You're using a bd integrator, so the relationships here are not as 
straightforward as with md or sd integrators.  I'm not experienced enough to 
comment on the implications of various settings for bd, but I would refer you to 
the manual, where the relationships are described (and how some of the .mdp 
keywords are used in special ways).

Generally speaking, if you want to conduct a simulation at a different 
temperature, changing gen_temp and ref_t are indeed all that are required.  The 
value of tau_t controls how tight the coupling is, nothing more.

-Justin

> Here is my mdp file:
> title        = OPLS Lysozyme NVT equilibration 
> ;define        = -DPOSRES    ; position restrain the protein
> ; Run parameters
> integrator    = bd        ; leap-frog integrator
> 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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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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