[gmx-users] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello,

I am copy pasting my "mdp" file for the last step of my procedure :

Here I am not using any freeze group.

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000        ; 100 ps
dt              = 0.002         ; 2 fs
energygrps      = Protein Non-Protein
; Output control
nstxout         = 10
nstvout         = 10
nstlog          = 10
nstenergy       = 10
nstxtcout       = 50
; Bond parameters
continuation    = yes           ; after trial 400 K
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           = 1.4           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.4           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.4           ; 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
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
ewald_rtol      = 1e-5 ; relative strength of Ewald - shifted direct
potential
optimize_fft    = yes ; saves computation time
; Temperature coupling is on
tcoupl          = V-rescale             ; modified Berendsen thermostat
tc-grps         = Non-Protein
tau_t           = 0.1           ; time constant, in ps
ref_t           = 300           ; reference temperature,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
; COM motion removal
; These options remove COM motion of the system
nstcomm         = 100
comm-mode       = Linear
comm-grps       = System


Plz have a look.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.