[gmx-users] Problem with Umbrella Sampling simulation
Daniele Veclani
danieleveclani at gmail.com
Fri Jul 22 16:17:54 CEST 2016
Dear Justin
I am really grateful for your help.
I have based my job on your tutorial, but I had to adapt it to my case study
. I also use a different version of gromacs.
I used .mdp your files as templates, but I have adapted to my problem.
Thanks for your help
Best regards,
D.V.
2016-07-22 15:56 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> ==================================================
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