# Re: [AMBER] Lipid diffusion in cpptraj

From: Life Sciences Inc <contact.lifesciences.inc.gmail.com>
Date: Thu, 9 Jul 2015 00:45:45 +0200

Thank you very much Daniel for your anwer, but still I am getting the empty
files for diff out in x , y and z direction, I am using amber15 tools with
the command diffusion 5.0 diff.out :1, I have uploaded input files as parm
filename.psf and trajectory as trajin filename.dcd. I think my commands are
correct, kindly let me know what can be the problem?

I am also trying to make my own program for MSD vs time plot but I am
confued with very basic question, being a beginner in this MD simulation
kindly ignore my trivial question.

I calculated lipid per area from Cpptraj and the values are in accordance
with experimental values and for calculating lipid per area one gets box
values of x and y which are then divided by half the number of lipids in
the system to get a area per lipid.

for calculating MSD one has to square the x and y values to get the
position at particular time steps

following is just an idea to calculate MD vs time in python

import numpy as np
r = np.sqrt(xdata**2 + ydata**2)
diff = np.diff(r) #this calculates r(t + dt) - r(t)
diff_sq = diff**2
MSD = np.mean(diff_sq)

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?.

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
> > _______________________________________________
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> > 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)
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 08 2015 - 16:00:03 PDT
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