normal Umbrella simulation

  • sumar
  • sumar's Avatar Topic Author
  • Visitor
6 years 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

Please Log in or Create an account to join the conversation.

More
6 years 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

Please Log in or Create an account to join the conversation.

  • sumar
  • sumar's Avatar Topic Author
  • Visitor
6 years 8 months ago - 6 years 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: 6 years 8 months ago by sumar. Reason: wrong coment

Please Log in or Create an account to join the conversation.

  • sumar
  • sumar's Avatar Topic Author
  • Visitor
6 years 8 months ago - 6 years 8 months ago #7323 by sumar
Replied by sumar on topic Umbrella simulation
-
Last edit: 6 years 8 months ago by sumar.

Please Log in or Create an account to join the conversation.

More
6 years 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?

Please Log in or Create an account to join the conversation.

  • sumar
  • sumar's Avatar Topic Author
  • Visitor
6 years 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

Please Log in or Create an account to join the conversation.

More
6 years 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.

Please Log in or Create an account to join the conversation.

More
6 years 8 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

Please Log in or Create an account to join the conversation.

Time to create page: 0.093 seconds