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From: <hannes.loeffler.stfc.ac.uk>

Date: Tue, 14 Jul 2015 06:42:40 +0000

Lateral diffusion simply means diffusion in the plane here. So if that is xy then obviously sqrt(x*x + y*y). The STFC routines provide a convenience ouput for this if you choose 'xy' to the stfcdiffusion command. Defining 'mask2' computes the MSD only between mask1 and mask2 based on the minimum distance within the lower and upper bounds.

________________________________________

From: Life Sciences Inc [contact.lifesciences.inc.gmail.com]

Sent: 13 July 2015 22:50

To: AMBER Mailing List

Subject: Re: [AMBER] Lipid diffusion in cpptraj

Thank you Daniel Roe , now the command to calculate diffusion is running ,

I was just missing the run at the end of command. Thank you very much for

your guidance.

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 ?

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. 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?

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
*

*> > > Å^2).
*

*> > > > diff.out_y.xmgr: Mean square displacement(s) in the Y direction (in
*

*> > > Å^2).
*

*> > > > diff.out_z.xmgr: Mean square displacement(s) in the Z direction (in
*

*> > > Å^2).
*

*> > > > diff.out_r.xmgr: Overall mean square displacement(s) (in Å^2).
*

*> > > > diff.out_a.xmgr: Total distance travelled (in Å).
*

*> > > > 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
*

*> > > > _______________________________________________
*

*> > > > AMBER mailing list
*

*> > > > AMBER.ambermd.org <javascript:;>
*

*> > > > http://lists.ambermd.org/mailman/listinfo/amber
*

*> > > >
*

*> > >
*

*> > >
*

*> > > --
*

*> > > -------------------------
*

*> > > 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
*

*> > >
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> 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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http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

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http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jul 14 2015 - 00:00:02 PDT

Date: Tue, 14 Jul 2015 06:42:40 +0000

Lateral diffusion simply means diffusion in the plane here. So if that is xy then obviously sqrt(x*x + y*y). The STFC routines provide a convenience ouput for this if you choose 'xy' to the stfcdiffusion command. Defining 'mask2' computes the MSD only between mask1 and mask2 based on the minimum distance within the lower and upper bounds.

________________________________________

From: Life Sciences Inc [contact.lifesciences.inc.gmail.com]

Sent: 13 July 2015 22:50

To: AMBER Mailing List

Subject: Re: [AMBER] Lipid diffusion in cpptraj

Thank you Daniel Roe , now the command to calculate diffusion is running ,

I was just missing the run at the end of command. Thank you very much for

your guidance.

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 ?

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. 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?

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:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jul 14 2015 - 00:00:02 PDT

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