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
--
========================================
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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