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From: Life Sciences Inc <contact.lifesciences.inc.gmail.com>

Date: Wed, 1 Jul 2015 16:11:56 +0200

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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AMBER.ambermd.org

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

Received on Wed Jul 01 2015 - 07:30:03 PDT

Date: Wed, 1 Jul 2015 16:11:56 +0200

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

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

Received on Wed Jul 01 2015 - 07:30:03 PDT

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