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 = 500000 ; 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 = 1.0 1.0 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.