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