[gmx-users] Problem with Umbrella Sampling simulation

[Justin Lemkul]

On 7/22/16 9:13 AM, Daniele Veclani wrote:
> Dear Justin
>
> Thank you for your answer.
>
> So I use this .mdp file for fast NPT equilibration:
> ; Run control
> integrator               = sd       ; Langevin dynamics
> dt                       = 0.002
> nsteps                   = 50000    ; 0.1 ns
> nstcomm                  = 10
> ; Output control
> nstxout                  = 500
> nstvout                  = 500
> nstfout                  = 500
> nstlog                   = 500
> nstenergy                = 100
> nstxout-compressed       = 500
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 0.8
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tcoupl                   = Nose-Hoover
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
> ; Pressure coupling is on for pull
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Free energy control stuff
> ; Generate velocities to start
> gen_vel                  = no
> gen_temp                 = 298.15
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 4
> lincs-iter               = 1
> ; Pull code
> pull                    = umbrella
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = B
> pull_group2_name        = A
> pullgeometry            = distance      ; simple distance increase
> pull_coord1_groups = 1 2
> pull_dim                = N Y N
> pull_coord1_rate        = 0.0          ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_start              = yes
>
> Then I use this .mdp file for Umbrella sampling simulation:
> ; Run control
> integrator               = sd       ; Langevin dynamics
> dt                       = 0.002
> nsteps                   = 500000    ; 1 ns
> nstcomm                  = 10
> ; Output control
> nstxout                  = 10000
> nstvout                  = 10000
> nstfout                  = 10000
> nstlog                   = 10000
> nstenergy                = 10000
> nstxout-compressed       = 10000
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 0.8
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tcoupl                   = Nose-Hoover
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
> ; Pressure coupling is on for pull
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Free energy control stuff
> ; Generate velocities to start
> gen_vel                  = no
> gen_temp                 = 298.15
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 4
> lincs-iter               = 1
> ; Pull code
> pull                    = umbrella
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = *B*
> pull_group2_name        = A
> pullgeometry            = distance      ; simple distance increase
> pull_coord1_groups = 1 2
> pull_dim                = N Y N
> pull_coord1_rate        = 0.0          ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_start              = yes
>
> These .mdp files are correct?
>
> I apologize for the inconvenience but this is the first time I try to do
> this kind of simulation.
>

Make sure you work through a highly controlled tutorial first:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

Aside from the position restraints (these are unique to the system I studied in 
the tutorial, so do not generally use them) the framework is the same and you 
can use the .mdp files as a template.  A one-dimensional restraint may also not 
be necessary; in general, restraining the distance between two entities is not 
directional but again my application was specific and there is a known 
directionality there.

-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

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