Re: [AMBER] Lipid diffusion in cpptraj

From: <hannes.loeffler.stfc.ac.uk>
Date: Fri, 31 Jul 2015 06:42:35 +0000

I have written the STFC diffusion code years back because I was interested in calculation this property in a certain region only. The code used to be (in ptraj) a direct clone of the older code. But as far as I remember the old code reported the components as well. Doesn't it do that anymore or does my memory fail me?
________________________________________
From: Life Sciences Inc [contact.lifesciences.inc.gmail.com]
Sent: 30 July 2015 22:22
To: AMBER Mailing List
Subject: Re: [AMBER] Lipid diffusion in cpptraj

Thank you Dan for helping me out , I tried both of the traditional
diffusion and stfcdiffusion commands to calculate lipid lateral diffusion.
But in my view lateral diffusion can only be calculated with stfc diffusion
command only by selecting xy.

and . hannes loeffler in my previous messages I posted short python snippet
to calculate MSD, I was wrong as the formula for MSD is [image:
\rm{MSD}\equiv\langle \left( x(t)-x_0\right)^{2}\rangle,] so MSD should be
calculated without taking the square root. Hope same approach without
taking square root is being used in both diffusion and stfcdiffusion of
Cpptraj to calculate MSD vs time...



On Tue, Jul 14, 2015 at 4:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> On Mon, Jul 13, 2015 at 3:50 PM, Life Sciences Inc <
> contact.lifesciences.inc.gmail.com> wrote:
>
> > I am directly running the command from terminal as diffusion 5.0 diff.out
> > :DOPC by directly loading the psf and trajectory in dcd format, I am
> > masking the DOPC as I have to calculate lipid diffusion for all the DOPC
> > lipids in my system. I have also unwrapped the trajectory. But if I use
> :1
> > for masking other than writing DOPC my results are little different, can
> > you please tell me why ?
> >
>
> The :DOPC mask chooses all residues named :DOPC, whereas :1 will choose
> only residue 1. If your trajectory were near-infinite the results should
> match, but as it is finite the behavior of an individual molecule can vary
> from the average (this is connected to why there is a 'Limit as time
> approaches infinity' in the Einstein relation).
>
>
> >
> > And correct me if I use a trajectory only having my lipids meaning
> > trajectory without water, ions or any other molecule then I dont think it
> > requires unwraping.
>
>
> Any time you calculate diffusion in a system that has PBC and you have
> performed imaging you need to unwrap. If a molecule is imaged from one side
> of a unit cell to the other that's hardly a physical transition, right?
>
>
> > I have stripped my trajectory of water and ions just to
> > save the memory in my computer as the whole trajectory with all atoms
> makes
> > my computer to halt. is this approach correct? if not then I should use
> > the unwrapped trajectory with all atoms?
> >
>
> You can strip, but make sure you save the box coords (i.e. do not use the
> 'nobox' keyword with the 'trajout' command). This way you can unwrap etc at
> will in subsequent calculations.
>
> -Dan
>
>
> >
> > My last question is that diffusion command in cpptraj gives results in
> all
> > directions x, y and z separately and with a.xmgr it gives the total
> > displacement in x y and z ? but I have to calculate lateral diffusion for
> > my lipids, should I use simple diffusion command or stfc command for
> that,
> > as I do not want to calculate diffusion for certain distances as
> mentioned
> > in stfc command . How can I correctly calculate lateral diffusion for my
> > system?
> >
> > waiting for your kind reply.
> >
> > Thanks Alot ....
> >
> > On Thu, Jul 9, 2015 at 5:15 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > I would need to see your entire cpptraj input and output to be sure,
> but
> > is
> > > it possible you are running these commands interactively? If so you
> need
> > to
> > > also type 'go' or 'run' to actually do any processing (if you're
> running
> > > cpptraj in batch mode, i.e. cpptraj -i input.file then a 'run' is
> implied
> > > at the end of input if one is not specified).
> > >
> > >
> > > On Wed, Jul 8, 2015 at 4:45 PM, Life Sciences Inc <
> > > contact.lifesciences.inc.gmail.com> wrote:
> > >
> > > >
> > > > Kindly correct me this x and Y values are not the box values from
> > > > trajectory? are these the position values from trajectory file or
> > > velocity?
> > > > and if yes then how to extract the position values from the
> trajectory
> > > > file?.
> > > >
> > >
> > > Diffusion is all about motion (translational/rotational) - it has
> nothing
> > > to do with box coordinates. Cpptraj makes use of the Einstein relation
> to
> > > calculation translational diffusion:
> > >
> > > 2*n*D = Lim(t->infinity)[ MSD / t]
> > >
> > > Where n is the number of dimensions you're calculating displacement in.
> > The
> > > mean square displacement for a coordinate is the sum of the square of
> the
> > > distances traveled in each frame from the previous frames (i.e. you're
> > > tracing the total dist^2 the coordinate has traveled over the course of
> > the
> > > simulation). It doesn't have anything to do with the box coordinates
> > > (although as mentioned in the manual you will want to 'unwrap' prior to
> > the
> > > diffusion calculation to avoid imaging jumps). You may want to review
> > some
> > > of the theory behind this before proceeding, IIRC the Leach Molecular
> > > Modelling book has a good description. It probably wouldn't hurt to
> > review
> > > the 'diffusion' command in the Amber15 manual as well.
> > >
> > > Hope this helps,
> > >
> > > -Dan
> > >
> > >
> > > >
> > > > Hope to get a positive response...
> > > >
> > > > On Thu, Jul 2, 2015 at 6:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You may want to try the 'stfcdiffusion' command instead as this can
> > > > > explicitly calculate diffusion in the XY plane (see manual for full
> > > > > syntax). Also make sure you are using the latest version of cpptraj
> > > (15).
> > > > >
> > > > > -Dan
> > > > >
> > > > > On Wednesday, July 1, 2015, Life Sciences Inc <
> > > > > contact.lifesciences.inc.gmail.com> wrote:
> > > > >
> > > > > > Dear all
> > > > > >
> > > > > > 1) I have two questions regarding lateral diffusion of lipids in
> a
> > > > > bilayer,
> > > > > > I want to calculate diffusion in two dimensions X and Y, how to
> > > > calculate
> > > > > > it in cpptraj?
> > > > > >
> > > > > >
> > > > > > I have total system with atoms 102220, total number of water
> 15640
> > > and
> > > > > 400
> > > > > > lipid molecules, 16140 residues, time per frame in my trajectory
> > is 5
> > > > > ps. I
> > > > > > want to calculate diffusion for all my lipid molecules in the
> > system.
> > > > > > After loading the topolgy file and unwraped trajectory in
> cpptraj I
> > > am
> > > > > > giving the following command to calculate diffusion for my lipid
> > > > > molecule .
> > > > > >
> > > > > > diffusion 5.0 diff.out :1
> > > > > >
> > > > > >
> > > > > > I get the following output which is normal;
> > > > > >
> > > > > > DIFFUSION:
> > > > > > Atom Mask is [:1]
> > > > > > The average and individual results will be printed to:
> > > > > > diff.out_x.xmgr: Mean square displacement(s) in the X direction
> > (in
> > > > > ^2).
> > > > > > diff.out_y.xmgr: Mean square displacement(s) in the Y direction
> > (in
> > > > > ^2).
> > > > > > diff.out_z.xmgr: Mean square displacement(s) in the Z direction
> > (in
> > > > > ^2).
> > > > > > diff.out_r.xmgr: Overall mean square displacement(s) (in ^2).
> > > > > > diff.out_a.xmgr: Total distance travelled (in ).
> > > > > > The time between frames in ps is 5.000.
> > > > > > To calculate diffusion constants from a mean squared displacement
> > > plot
> > > > > > (i.e. {_x|_y|_z|_r}.xmgr), calculate the slope of the line and
> > > multiply
> > > > > > by 10.0/6.0; this will give units of 1x10^-5 cm^2/s
> > > > > >
> > > > > > but;
> > > > > >
> > > > > > whenever I open xmgr files they are empty and of 0 bytes size. I
> > > cannot
> > > > > > understand what is happening, can anyone let me know where I am
> > > making
> > > > > the
> > > > > > mistake.
> > > > > >
> > > > > > 2) I want to calculate lipid jumps throughout the system as well
> if
> > > > > anyone
> > > > > > have scripts or did such analysis kindly guide me;
> > > > > >
> > > > > > My idea is to calculate centre of mass for the system and then
> > from
> > > > > that
> > > > > > centre of mass around it jumps/lateral dffusion in specific
> > direction
> > > > can
> > > > > > be calculated say 5 angstrom around COM and in this way for the
> > whole
> > > > > > system. I think stfcdiffusion is somewhat close to my idea but I
> > dont
> > > > > know
> > > > > > how to calculate the COM and what should be the total distance in
> > > > which I
> > > > > > have to calculate the diffusion (by dividing in to shorter
> > distances
> > > > and
> > > > > > for each distance diffusion from COM must be calculated, int his
> > way
> > > > for
> > > > > > the whole system ).
> > > > > >
> > > > > > I would be really grateful for any help
> > > > > > _______________________________________________
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> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > -------------------------
> > > > > Daniel R. Roe, PhD
> > > > > Department of Medicinal Chemistry
> > > > > University of Utah
> > > > > 30 South 2000 East, Room 307
> > > > > Salt Lake City, UT 84112-5820
> > > > > http://home.chpc.utah.edu/~cheatham/
> > > > > (801) 587-9652
> > > > > (801) 585-6208 (Fax)
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> > > >
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 307
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
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> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 31 2015 - 00:00:03 PDT
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