I think that may well be the case. The polymer would move freely towards and away from the bilayer in the Z direction but would never diffuse or get close enough to interact. I've just run a simulation placing the polymer in a tight space with a bilayer above and below it and theres barely any movement of the polymer along the Z axis, its seems that there's something 'repelling' it any time it gets close to the bilayer. I've attached a text version of my mdp file, I would like to attach snapshots of my system setup but it would exceed the 50 KB limit. Thanks Alex
> Date: Tue, 12 Aug 2014 17:15:25 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Polymer not diffusing into membrane > > > > On 8/12/14, 1:35 PM, Alex s wrote: > > I've run it for 200 ns which I think is long enough allow the polymer to > > diffuse. > > > > If, as you say, it "never interacts or diffuses," it suggests that you're > applying some sort of restraint. Without seeing .mdp files and some sort of > quantitative measure of what you're seeing, it's hard to comment further. > Images would also be helpful. It depends on the size of the system and the > initial distance, but I would think you'd need far less than 200 ns to see > such > an interaction. > > -Justin > > >> Date: Tue, 12 Aug 2014 10:41:52 +0200 > >> From: deviceran...@gmail.com > >> To: gmx-us...@gromacs.org > >> Subject: Re: [gmx-users] Polymer not diffusing into membrane > >> > >> How long is your simulation? Are you sure it is long enough to see what you > >> want to see? > >> On 12 Aug 2014 07:15, "Alex s" <as1...@hotmail.com> wrote: > >> > >>> Dear Gromacs users > >>> I'm not sure if this a question suitable for this forum but I would > >>> greatly appreciate it if you can help me in anyway regarding this issue. > >>> I've have a system made up of a lipid bilayer, water and a single chain > >>> polymer. My aim is to place the polymer just above the lipid bilayer in > >>> the water phase and let it diffuse into the bilayer. This polymer has been > >>> shown to interact with the lipid bilayer in previous studies us. The issue > >>> I'm having is that in my simulation the polymer stays in the water phase > >>> just hovering above the lipid membrane and never interacts or diffuses. > >>> I've tried simulating it in a number of different ways by varying the > >>> number of water molecules, changing box size or polymer position however I > >>> haven't had any success yet. The main steps in setting up my system is as > >>> follows: > >>> 1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the final > >>> box size of the lipid bilayer and use it to place the Polymer at specific > >>> point just above the lipid bilayer. 3. Perform energy minimization on the > >>> system4. Perform NVT and NPT5. Run the simulation > >>> Any advice would be helpful > >>> Regards > >>> Alex > >>> -- > >>> 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. > >>> > >> -- > >> 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. > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.040 nsteps = 1250000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 100 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = DPPC POL W ION ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 1.0 1.0 1.0 ref_t = 325 325 325 325 325 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 0.2 0.2 0.2 0.2 compressibility = 3e-5 3e-5 3e-5 3e-5 ref_p = 1.0 1.0 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 105 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30
-- 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.
