From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jan 27 2016 - 09:22:40 CST
Hi,
The simplest solution would be to turn wrapAll off, since what is
happening is that the center of mass of the segment (in this case just
the ligand) is going across the periodic boundary edge and NAMD is
wrapping the position around to the origin. However, since the
simulation has already been run, what I would recommend is to load it in
VMD, and unwrap just the ligand, and then save the trajectory again. See
the pbctools plugin
(http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/). This command
*should* bring the ligand back to where you expect it.
pbc unwrap -sel "text to select the ligand in VMD"
-Josh Vermaas
On 01/27/2016 07:54 AM, R. Charbel MAROUN wrote:
> Hello NAMD users:
>
> I have a receptor embedded in a lipid bilayer. The receptor has a
> ligand in its binding site. After several hundred ps of MD, the
> receptor (and the ligand) move away from the center of the membrane in
> the plane of the membrane. As I have applied PBC, when the receptor
> gets away far enough from the membrane, its image appears at the other
> side. Sometimes, it's the image of the ligand that appears in the
> other side. This depends on whether the receptor or the ligand attains
> the border of the cell. As a consequence, the receptor and ligand get
> unpaired for many frames, ie, the ligand is not in the binding site.
> Apparently, the ligand continues to behave as if in it. The problem
> comes if I want to measure, for ex., distances between ligand and
> residues for those frames, or make statistics out of my trajectory.
> Below is the inp file I'm using.
>
> Is there any way around, such as imposing a constraint to the ligand,
> so that it follows the receptor, even if the ligand doesn't "hit" the
> border of the cell ?
>
>
>
> structure C_3CAP-H2ODow-HME_sol_ion.psf
> coordinates C_3CAP-H2ODow-HME_sol_ion.pdb
>
> outputName step74_prod; # base name for output from this run
> # NAMD writes two files at the
> end, final coord and vel
> # in the format of
> first-dyn.coor and first-dyn.vel
>
> set inputname step73_prod;
> binCoordinates $inputname.restart.coor; # coordinates from last
> run (binary)
> binVelocities $inputname.restart.vel; # velocities from last
> run (binary)
> extendedSystem $inputname.restart.xsc; # cell dimensions from
> last run (binary)
>
> firsttimestep 2254880; # last step of previous run
> restartfreq 500; # 500 steps = every 1ps
> dcdfreq 1000;
> dcdUnitCell yes; # the file will contain unit
> cell info in the style of
> # charmm dcd files. if yes, the
> dcd files will contain
> # unit cell information in the
> style of charmm DCD files.
> xstFreq 500; # XSTFreq: control how often
> the extended systen configuration
> # will be appended to the XST file
> outputEnergies 125; # 125 steps = every 0.25ps
> # The number of timesteps
> between each energy output of NAMD
> outputTiming 500; # The number of timesteps
> between each timing output shows
> # time per step and time to
> completion
>
> # Force-Field Parameters
> paraTypeCharmm on; # We're using charmm type
> parameter file(s)
> # multiple definitions may be
> used but only one file per definition
>
> # parameters
> /usr/local/vmd-.9/lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
>
> parameters
> /home/cmaroun/toppar/toppar_27/par_all27_prot_lipid_cholesterol_HME_TIP3.prm
> parameters /home/cmaroun/readcharmmpar1.2/par_all36_lipid.prm
>
> # These are specified by CHARMM
> exclude scaled1-4 # non-bonded exclusion policy
> to use "none,1-2,1-3,1-4,or scaled1-4"
> # 1-2: all atoms pairs that are
> bonded are going to be ignored
> # 1-3: 3 consecutively bonded
> are excluded
> # scaled1-4: include all the
> 1-3, and modified 1-4 interactions
> # electrostatic scaled by
> 1-4scaling factor 1.0
> # vdW special 1-4 parameters in
> charmm parameter file.
> 1-4scaling 1.0
> switching on
> vdwForceSwitching yes; # New option for force-based
> switching of vdW
> # if both switching and
> vdwForceSwitching are on CHARMM force
> # switching is used for vdW
> forces.
>
> # You have some freedom choosing the cutoff
> cutoff 12.0; # may use smaller, maybe 10.,
> with PME
> switchdist 10.0; # cutoff - 2.
> # switchdist - where you start
> to switch
> # cutoff - where you stop
> accounting for nonbond interactions.
> # correspondence in charmm:
> # (cutnb,ctofnb,ctonnb =
> pairlistdist,cutoff,switchdist)
> pairlistdist 14.0; # stores the all the pairs with
> in the distance it should be larger
> # than cutoff( + 2.)
> stepspercycle 20; # 20 redo pairlists every ten
> steps
> pairlistsPerCycle 2; # 2 is the default
> # cycle represents the number
> of steps between atom reassignments
> # this means every 20/2=10
> steps the pairlist will be updated
>
> # Integrator Parameters
> timestep 2.0; # fs/step
> rigidBonds all; # Bound constraint all bonds
> involving H are fixed in length
> nonbondedFreq 1; # nonbonded forces every step
> fullElectFrequency 1; # PME every step
>
> wrapWater on; # wrap water to central cell
> wrapAll on; # wrap other molecules too
> wrapNearest off; # use for non-rectangular cells
> (wrap to the nearest image)
>
> # PME (for full-system periodic electrostatics)
> source checkfft.str
> margin 2.5;
> PME yes;
> PMEInterpOrder 6; # interpolation order (spline
> order 6 in charmm)
> PMEGridSizeX $fftx; # should be close to the cell size
> PMEGridSizeY $ffty; # corresponds to the charmm
> input fftx/y/z
> PMEGridSizeZ $fftz;
>
> # Constant Temperature Control
> set temp 323.15;
> langevin on; # langevin dynamics
> langevinDamping 1.0; # damping coefficient of 1/ps
> (keep low)
> langevinTemp $temp; # random noise at this level
> langevinHydrogen no; # don't couple bath to hydrogens
> reinitvels $temp;
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes; # use a hydrogen-group based
> pseudo-molecular viral to calcualte pressure and
> # has less fluctuation, is
> needed for rigid bonds (rigidBonds/SHAKE)
> useFlexibleCell yes; # yes for anisotropic system
> like membrane
> useConstantRatio yes; # keeps the ratio of the unit
> cell in the x-y plane constant A=B
>
> langevinPiston on; # Nose-Hoover Langevin piston
> pressure control
> langevinPistonTarget 1.0; # target pressure in bar 1atm =
> 1.01325bar
> langevinPistonPeriod 50.0; # oscillation period in fs.
> correspond to pgamma T=50fs=0.05ps
> # f=1/T=20.0(pgamma)
> langevinPistonDecay 25.0; # oscillation decay time.
> smaller value correspons to larger random
> # forces and increased coupling
> to the Langevin temp bath.
> # Equall or smaller than piston
> period
> langevinPistonTemp $temp; # coupled to heat bath
> run 1500000; # 3ns
>
>
>
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