On 2/28/19 2:09 PM, Javad Deylami wrote:
Hi Justin,
I have one general and one specific question about doing the pulling
simulation.
Can you let me know how I should choose pull_coord1_geometry among
distance, direction, and cylinder? How can I distinguish these three
geometries to use them in different systems? How can different choices
affect the outcome (PMF curve)?
In principle, they can all be used to achieve equivalent results, though
the cylinder geometry is largely designed for membranes and is described
in detail in the manual.
Which methos you recomment to pull a molecule acroos the bilayer? why?
In my case, I want to calculate the permeability of ion in a specific
bilayer. I faced this error: Can not have dynamic box while using pull
geometry 'direction-periodic' (dim z)
I found you already replied the similar issue: *"align the system such that
you are pulling along z, in conjunction with semi-isotropic coupling and
zero compressibility along z."*
Can you explain how I should do that alignment in my pull code?
The alignment has nothing to do with the pull code. It means the initial
coordinates should be aligned such that your reaction coordinate is
coincident with the z-axis. For a typical lipid membrane, the membrane
normal is already aligned along z since the membrane is in x-y. Then you
just place your molecule of interest directly above the membrane.
-Justin
This is my pull code:
title = Umbrella pulling simulation
define = -DDPPC_O
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 50; 1000 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes ; continuing from NPT
; Single-range cutoff scheme
cutoff-scheme = Verlet
nstlist = 20
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 = Nose-Hoover
tc_grps = MEMB SOL_ION
tau_t = 1.01.0
ref_t = 303.15 303.15
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
refcoord_scaling = com
; 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_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 2 ; two groups defining one reaction
coordinate
pull_group1_name= CAL
pull_group2_name= DPPC_O
pull_coord1_type= umbrella ; harmonic potential
pull_coord1_geometry= distance ; simple distance increase
pull-geometry = direction-periodic
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull-coord1-vec = 0 0 1
pull-coord1-init= 0 ;
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Your attention is highly appreciated.
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
