[gmx-users] Re: umbrella sampling

[Vijayaraj]

Hi Justin,

Here is my complete code for umbrella sampling

title       = Umbrella pulling simulation
define      = -DPOSRES_2

integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 2500000   ; 5 ns
nstcomm     = 10
nstxout     = 50000     ; every 100 ps
nstvout     = 50000
nstfout     = 5000
nstxtcout   = 5000      ; every 10 ps
nstenergy   = 5000

constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes

nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4

; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes

; Berendsen temperature coupling is on in two groups
Tcoupl      = V-rescale
tc_grps     = Protein   SOL
tau_t       = 0.5       0.5
ref_t       = 300       300

; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0

; Generate velocities is off
gen_vel     = no

; Periodic boundary conditions are on in all directions
pbc     = xyz

; Long-range dispersion correction
DispCorr    = EnerPres

; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 1000
pull_nstxout    = 1000
pull_nstfout    = 1000


I will do this umbrella sampling for 10ns,
Do you think the COM distance can converge after long simulation time? ie
back to the restraint position.

Regards,
Vijay.




> Vijayaraj wrote:
> > Hello,
> >
> > I am doing umbrella sampling to calculate PMF curve for the detachment
> > of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled
> > cyclic peptide nanotube. I extracted the reaction coordinates staring
> > from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5
> > ang, I did umbrella sampling on 25 configurations (for 5ns) and the
> > window size is 0.5 ang. I used the following pulling code for umbrella
> > sampling,
> >
> > pull            = umbrella
> > pull_geometry   = distance
> > pull_dim        = N N Y
> > pull_start      = yes
> > pull_ngroups    = 1
> > pull_group0     = Chain_B
> > pull_group1     = Chain_A
> > pull_init1      = 0
> > pull_rate1      = 0.0
> > pull_k1         = 1000
> > pull_nstxout    = 1000
> > pull_nstfout    = 1000
> >
> >
> > I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM
> > distance between the chain_A (terminal) and chain_B (2nd CP) should be
> > restrained. after 5ns of umbrella sampling, I calculated the COM
> > distance between chain A and B, but it was not restrained, for the 5.5
> > ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang.
> > and also the pulling cyclic peptide undergoes large conformational
> > sampling. from the WHAM analysis I understood the sampling window is
> > poorly represented. In addition to COM distance restrain, can I restrain
> > the pulling CP's backbone atoms? so that the pulling groups large
> > conformational sampling will be reduced.
>
> You could implement dihedral restraints to fix the backbone secondary
> structure,
> but I can't comment on the stability of trying to use these restraints in
> addition to the pull code.  Seems like a lot going on at once, to me.
>
> Also consider the fact that 5 ns is an extremely short timeframe to gather
> meaningful data.  Perhaps you just need more time in each window to
> equilibrate.
>  At the shortest COM distance, your two molecules are still likely
> experiencing
> some interactions, and it may require a great deal of sampling in this
> window to
> converge the simulations.  You haven't shown the rest of your .mdp file
> (always
> a good idea!), so we can only guess at whether or not your other settings
> should
> lead to a sensible result.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111028/4062e916/attachment.html>