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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 9 Jul 2015 09:15:59 -0600

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
*

*>
*

Date: Thu, 9 Jul 2015 09:15:59 -0600

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:

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

-- ------------------------- 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/amberReceived on Thu Jul 09 2015 - 08:30:03 PDT

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