[gmx-users] Problem with Umbrella Sampling simulation
Daniele Veclani
danieleveclani at gmail.com
Fri Jul 22 15:13:17 CEST 2016
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.
Best regards,
D.V.
2016-07-22 14:23 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 7/22/16 8:19 AM, Daniele Veclani wrote:
>
>> Dear Gromacs Users
>>
>> I'm trying to calculate the potential mean force between two molecules (A
>> and B).
>>
>> I created the various configurations through the pull simulation. To do
>> this I kept fixes the position of the molecule A (position restraint)
>>
>> I have extracted the coordinates and sampled the various configurations.
>>
>> Now I have to use these configurations as input for umbrella sampling
>> simulation.
>>
>> I have a couple of questions:
>>
>> - Do I have to maintain a position restraint on A molecule?
>>
>>
> No.
>
> - Do I have to enter the position restraint even for molecule B? (Otherwise
>> during the dynamic simulation I a change of the distance between molecule
>> A
>> and B)
>>
>>
> No. The distance between A and B is all that matters and it is restrained
> using the harmonic potential applied by the pull code. It will vary over
> time but should on average, in each window, be equal to the restraint
> reference distance specified in the .mdp file.
>
> -Justin
>
> - Can I get a clear explanation about this last step of the job?
>>
>> Best regards,
>> D.V.
>>
>>
> --
> ==================================================
>
> 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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