normal Umbrella simulation

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1 year 8 months ago #7320 by sumar
Umbrella simulation was created by sumar
Hi all

I would like to do umbrella simulation to calculate PMF a complex system consisted of peptide and bilayer membrane of POPC. I tried to search some tutorials in MARTINI website but I did not find it. Could you tell me how could I do this simulation? what kind of mdp files that I need to execute this simulation?

regards
Sumar

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1 year 8 months ago #7321 by peterkroon
Replied by peterkroon on topic Umbrella simulation
Hi Sumar,

take a normal Martini mdp file, and just add your pulling parameters to it. You can follow e.g. this tutorial[1] to get a grasp of umbrella sampling in Gromacs. Even though the tutorial is atomistic, the ideas are directly transferrable.

Peter

[1] www.bevanlab.biochem.vt.edu/Pages/Person.../umbrella/index.html

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1 year 8 months ago - 1 year 8 months ago #7322 by sumar
Replied by sumar on topic Umbrella simulation
I have added pull parameter in my npt.mdp

; Pull code
pull = umbrella ;yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = POPC ;Chain_B
pull_group2_name = Protein ;Chain_A
pull-coord1-type = umbrella ; harmonic biasing force
pull-coord1-geometry = distance ; simple distance increase
pull-geometry = direction-periodic
pull-coord1-groups = 1 2
pull-coord1-dim = N N Y
pull-coord1-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k = 1000 ; kJ mol^-1 nm^-2
pull-coord1-start = yes ; define initial COM distance >

eventually, I get some errors, those paramaters are unknow in gromacs.
Last edit: 1 year 8 months ago by sumar. Reason: wrong coment

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1 year 8 months ago - 1 year 8 months ago #7323 by sumar
Replied by sumar on topic Umbrella simulation
-
Last edit: 1 year 8 months ago by sumar.

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1 year 8 months ago #7324 by peterkroon
Replied by peterkroon on topic Umbrella simulation
At a glance it looks sane. Did you give grompp an index file defining the groups POPC and Protein? Which version of Gromacs are you using?

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1 year 8 months ago #7325 by sumar
Replied by sumar on topic Umbrella simulation
yes I did.

tcoupl = Berendsen ; Nose-Hoover ;v-rescale
tc-grps = Protein POPC W_ION
tau_t = 1.0 1.0 1.0
ref_t = 320 320 320
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = yes ;no
gen_temp = 320
gen_seed = 473529


We use gromacs version 5.0.4

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1 year 8 months ago #7326 by peterkroon
Replied by peterkroon on topic Umbrella simulation
manual.gromacs.org/archive/5.0.7/online/mdp_opt.html#pull

It should be pull-start = yes instead of pull-coord1-start = yes. If you need more help post the full mdp, exact grompp call and its output.

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1 year 7 months ago #7327 by riccardo
Replied by riccardo on topic Umbrella simulation
You'll have to convert the directives in Justin Lemkul's tutorial to their GMX 5 analogous. Here some I use:

; COM pulling
pull = yes ; yes or no
; the number of pull coordinates
pull-ncoords = 1
; Groups to pull
pull-ngroups = 2
pull-group1-name = GROUP1
pull-group2-name = GROUP2
pull-coord1-groups = 1 2 ; see permalink.gmane.org/gmane.science.biology.gromacs.user/67963 for doubts
; Pull type: umbrella, constraint, constant-force, flat-bottom, ...
pull-coord1-type = umbrella
; Pull geometry: distance, direction, cylinder or position
pull-coord1-geometry = distance
; Select components for the pull vector. default: Y Y Y
pull-coord1-dim = Y Y Y ; 3 dimensions
; Init, rate, k (J/mol*nm^2)
pull-coord1-init = FILL_IN_A_DISTANCE
pull-coord1-k = 1500
pull-coord1-start = no ; do not modify pull-coord1-init
pull-coord1-rate = 0

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