mohsen ramezanpour wrote:
Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use
grompp this warning is occuring.
The only reason I can see for this occurring is that you're using an ancient
(pre-4.0) version of Gromacs.
-Justin
WARNING 1 [file configuration.mdp, line unknown]:
Unknown left-hand 'continuation' in parameter file
WARNING 2 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull' in parameter file
WARNING 3 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_geometry' in parameter file
WARNING 4 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_dim' in parameter file
WARNING 5 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_start' in parameter file
WARNING 6 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_ngroups' in parameter file
WARNING 7 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_group0' in parameter file
WARNING 8 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_group1' in parameter file
WARNING 9 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_rate1' in parameter file
WARNING 10 [file configuration.mdp, line unknown]:
Unknown left-hand 'pull_k1' in parameter file
I copy my .mdp file.where of it is wrong??
title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 250000 ; 500 ps
nstcomm = 1
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N Y N
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = protein
pull_group1 = LIG
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
thanks in advance
Mohsen
--
========================================
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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