From: R. Charbel MAROUN (charbel.maroun_at_inserm.fr)
Date: Thu Jan 28 2016 - 05:26:33 CST
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.
--- 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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