[gmx-users] Pulling Mechanics
Alexander Yang
ahy3nz at virginia.edu
Mon Jan 16 21:04:42 CET 2017
On 1/13/17 6:37 PM, Alexander Yang wrote:
> > Hi everyone,
> >
> > I am pulling a water molecule into a bilayer using an absolute reference
> > (mdp file below). I have tried to adapt methodology in Justin Lemkul's
> > umbrella sampling tutorial, but I have encountered a couple issues:
> >
>
> If you're trying to get water to move into a bilayer, why are you using an
> absolute restraint? Intuitively, the groups should be the bilayer and the
> water.
>
My goal is to construct an excess free energy profile of water (in the
z-direction) in these bilayer systems to compare permeability. I'm using a
z-constraining method that involves pulling a single water molecule to
various z-coordinates (depths in the bilayer), constraining that molecule,
and recording the forces on that molecule. My idea has been to use an
absolute reference to anchor the water molecule to a particular
z-coordinate while still being free to roam in the xy-plane. I'm not trying
to introduce extra forces on the bilayer system itself to pull a water
molecule inside.
> > 1) The bilayer (already well-equilibrated) is either being pulled or
> > drifting. Without the pull code, the bilayer does not move. I've defined
> > center of mass motion removal for the non-waters, which I would expect to
> > keep the bilayer still. I've copied the mdp file below (Tracer2117
> > corresponds to 2117SOL, but I've defined the Tracer2117 group in the
> index
> > file as the 3 atoms that correspond to this water)
> >
>
> Applying COM motion removal to one group and not another is highly
> artificial.
> Couple that with your use of an absolute restraint (also somewhat
> artificial)
> and you're layering bad things upon bad things.
>
Because I was using an absolute reference, I was hoping to keep the
equilibrated bilayer still so the profile could be accurately constructed
for a profile of z-coordinates.
>
> -Justin
>
> > 2) I'm getting an error that the distance between the pull groups is
> larger
> > than 0.49 times the box size (the box is about 6.12 nm x 5.17 nm x 7.42
> > nm). The origin of my absolute reference is only 0.1 nm away from the
> water
> > molecule. The way I've specified my pull-coord-rate, at the timestep when
> > the pull distance is larger than half the box size, the distance between
> > the origin of the reference at time 0 and the water molecule at time of
> > crash exceeds half the box size. Is the reference position actually
> moving,
> > or does the pull-coord-rate specify a change to a quantity besides the
> > reference position such that the water molecule can be pulled while the
> > reference position stays where it originally was specified?
> > @ time 0 ns: Water (3.794, 1.447, 1.150), reference origin (3.794, 1.447,
> > 1.250)
> > @ crash (time 47.19ns): Water(3.997, 0.032, 4.751). My pull-coord-rate is
> > 7.7e-5 nm/ps, so would the reference be at (3.794, 1.447, 4.883)? If this
> > is the case, I'm not sure how this distance violates the box size rule.
> > However, the distance between reference @ t=0 and water @ t = 47.19ns,
> > violates the 0.49 box size rule.
> >
> >
> >
> > ******* Mdp File ***********
> >
> > Run MDP parameters
> >
> > integrator = md
> >
> > dt = 0.002
> >
> > nsteps = 25000000
> >
> > comm-mode = Linear
> >
> > nstcomm = 1
> >
> > comm-grps = non-water
> >
> >
> > ; Output parameters
> >
> > nstxout = 0
> >
> > nstvout = 0
> >
> > nstxtcout = 5000
> >
> > nstenergy = 5000
> >
> > nstlog = 5000
> >
> > nstfout = 0
> >
> >
> > ; Bond parameters
> >
> > continuation = yes
> >
> > constraint-algorithm = lincs
> >
> > constraints = all-bonds
> >
> > lincs-iter = 1
> >
> > lincs-order = 4
> >
> >
> > ; Neighbor searching
> >
> > cutoff-scheme = Verlet
> >
> > nstlist = 10
> >
> > rcoulomb = 1.4
> >
> > rvdw = 1.4
> >
> >
> > ; Electrostatics
> >
> > coulombtype = PME
> >
> > fourierspacing = 0.16
> >
> > pme_order = 4
> >
> >
> > ; Temperature coupling
> >
> > tcoupl = nose-hoover
> >
> > tc_grps = non-water water
> >
> > tau_t = 0.4 0.4
> >
> > ref_t = 305 305
> >
> >
> > ; Pressure coupling
> >
> > pcoupl = Parrinello-Rahman
> >
> > pcoupltype = isotropic
> >
> > tau_p = 2.0
> >
> > ref_p = 1.0
> >
> > compressibility = 4.5e-05
> >
> > refcoord_scaling = com
> >
> >
> > ; Misc stuff
> >
> > gen_vel = no
> >
> > pbc = xyz
> >
> > DispCorr = EnerPres
> >
> >
> > ; Pull parameters
> >
> > pull = yes
> >
> > pull-nstxout = 5000
> >
> > pull-nstfout = 5000
> >
> > pull-ngroups = 1
> >
> > pull-ncoords = 1
> >
> > pull-group1-name = Tracer2117
> >
> > pull-coord1-groups = 0 1
> >
> > pull-coord1-type = umbrella
> >
> > pull-coord1-geometry = direction
> >
> > pull-coord1-origin = 3.794 1.447 1.250
> >
> > pull-coord1-dim = N N Y
> >
> > pull-coord1-rate = 7.7e-05
> >
> > pull-coord1-vec = 0 0 1
> >
> > pull-coord1-k = 500.0
> >
> > pull-coord1-start = no
> >
> > *************
> >
> > I've attached URLS to snapshots below (time0 and time47). Red is water,
> > grey is the lipid bilayer, yellow is the water molecule (enlarged for
> > visibility), and I've placed axes in the center. Before the crash, the
> > water molecule was definitely moving in the correct direction (positive
> z).
> > The bilayer drifted in the direction the water molecule was moving.
> >
> > (time0) http://imgur.com/a/jWu33
> >
> > (time47) http://imgur.com/a/nekmL
> >
> > Thanks for the help,
> >
> > Alex
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 15 Jan 2017 12:50:52 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein-Ligand Complex MD simulation ;
> Command for Number of Hydrogen bond plo
> Message-ID: <f01a0916-e7c5-a06a-4699-0a93db6aa1ed at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/13/17 10:51 PM, Adarsh V. K. wrote:
> > Dear all,
> >
> > Protein-ligand complex MD simulation using Gromacs 5.1.4
> >
> > Can you please tell me command for Number of Hydrogen bond plot? and
> > Other interactions between protein and ligand?
> >
>
> gmx hbond calculates hydrogen bonds. Select the protein and the ligand to
> get
> the number of hydrogen bonds between them.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 15 Jan 2017 12:52:00 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] permeation events- ion channels in bilayer
> Message-ID: <cff0b0c0-0414-83ff-61f3-2dbf1d671b83 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/14/17 7:18 AM, Alex Mathew wrote:
> > Dear GMX users,
> >
> > We are looking for water permeation events across the ion-channel, which
> is
> > embedded in lipid bilayer. After one micro second MD simulation in
> > Gromacs2016.1 i used the below script for calculating the permeation
> > events,
> >
> > http://www.ks.uiuc.edu/Training/Tutorials/science/
> > nanotubes/files/permeation.tcl
> >
> > Unfortunately all the time it gives zero value (I have tried for
> different
> > upperEnd and lowerEnd ), but i can visualize the water movements in VMD
> > screen.
> >
> > Kindly provide your valuable suggestions, since i don't have much
> expertise
> > in coding/programming.
> >
>
> If you define permeation as a water moving into the core of the membrane or
> channel, you can use gmx select to calculate appropriate upper and lower
> boundaries (based on, e.g. upper and lower leaflet P coordinates or some
> suitable amino acids that define the boundaries of the channel) and then
> calculate the number of waters that have an oxygen with a z-coordinate
> between
> these boundaries.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 15 Jan 2017 12:54:01 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Adding new residue - modified LYS
> Message-ID: <8676dd45-cd80-5ffb-9fbb-0e40cfc17fcc at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/17 2:38 PM, Dan Si wrote:
> > Hi,
> >
> >
> >
> > I'm struggling with adding a new residue to my MD simulation. I would
> like
> > to create a residue (let's call it NML) that would be an original lysine
> > (LYS) residue with methyl group attached to it's amide bond nitrogen. I'm
> > using amber99sb-ildn force field for my simulations. Unfortunately, I'm
> very
> > new in using gromacs, so I would appreciate really !step-by-step!
> tutorial :
> > -)
> >
> >
> >
> >
> > Do I need to perform QM calculation to obtain some of the parameters? If
> > yes, should I use zwitter-ionic structure NH3-CH-(R)-C-(O)-O in the
> > optimization?
> >
>
> What do you learn from reading the AMBER99sb-ILDN paper (and preceding
> literature) regarding AMBER parametrization methodology?
>
> >
> >
> >
> > I understand, I need to specify the topology of the new residue and
> > parameters according to amber99sb-ildn force field, but how exactly am I
> > suppose to do it? Which files I need to modify before running pdb2gmx and
> > how?
> >
>
> http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> --
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