[gmx-users] pulling

[Justin A. Lemkul]

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
> 

-- 
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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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