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

[Justin Lemkul]

On 4/26/15 8:25 PM, Agnivo Gosai wrote:
> 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

What you want is:

tc-grps	= Protein Non-Protein
tau-t	= -1      0.1
ref-t	= 300     300

The ref-t for Protein is irrelevant since tau-t = -1 (as described in 
http://manual.gromacs.org/online/mdp_opt.html#tc).

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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