From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jan 28 2016 - 09:43:21 CST
Just a quick question, do you have the whole trajectory loaded? I have
to admit, I'm a bit fuzzy on the algorithm of how unwrap works, but
there is a way of getting pbctools to do what you want. Play around with
it first (Norman's suggestion also looked good), since its much cheaper
to rewrap the trajectory than to run another simulation!
-Josh
On 01/28/2016 05:26 AM, R. Charbel MAROUN wrote:
> Hello namders,
>
> Following Josh's proposition, I used
> pbc unwrap -sel "resname HME"
> where HME is the name of the ligand.
>
> pbc is unwrapping HME from its present receptor-unpaired positions.
> That's leading in many cases to other receptor-unpaired positions
> rather than to the original receptor-paired positions. I guess this is
> due to the fact that pbc cannot know what was the original unwrapped
> position of the ligand.
>
> So, back to the first stage.
>
> Cheers,
> ---
> R. Charbel MAROUN, Ph.D., H.D.R.
> UMR-S INSERM U1204/UEVE
> Structure et activité des biomolécules
> normales et pathologiques
> Université d'Evry-Val d'Essonne
> Bâtiment Maupertuis
> Rue du Père Jarlan
> 91000 EVRY
> FRANCE
> Tél: +33 1 69 47 76 64
> FAX: +33 1 69 47 02 19
> e-mail charbel.maroun_at_inserm.fr
>
> Le 27-01-2016 16:22, Josh Vermaas a écrit :
>> 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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