[gmx-users] md_pull code in umbrella sampling

[Justin Lemkul]

On 3/3/14, 12:33 AM, Arunima Shilpi wrote:
> Dear Sir
>   I am trying to calculate the potential mean force (PMF) between protein
> and Ligand. I have applied position restrain to protein. I have applied
> reference pulling group to Protein and Pulling force has been applied to
> ligand. The pul force is applied along Z-axis. I had query as to whether I
> am proceeding in the right direction. Here I have provided the detail of
> the content of md_pull.mdp
>

No one knows whether this is the correct approach but you.  We know nothing 
about the geometry of the system, and it appears you are likely trying to 
shoehorn my tutorial into whatever your system is.  Restraints on the protein 
are almost never necessary, especially during umbrella sampling of 
protein-ligand complexes.  The tutorial is a special case; don't try to apply it 
verbatim.  Further, unless you have aligned the reaction coordinate with the 
z-axis prior to doing any pulling or umbrella sampling, it is almost certain 
that a simple pull along z is not correct.  But again, that's only something you 
know.

-Justin

> md_pull.mdp
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_Protein
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 ps
> nstcomm     = 10
> ; 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       = 0.5       0.5
> 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
> refcoord_scaling = com
> ; 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  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = DRG
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> Regards
>
>
> Arunima
>

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================