[AMBER] Calculating lipid diffusion

From: Vijyan Achari <vjrajamani.yahoo.co.uk>
Date: Wed, 20 Aug 2014 03:07:36 +0100

Dear Sir/Madam, I am calculating diffusion of lipids in a bilayer using cpptraj command from Ambertools_14.  Since I have simulated for around 300 ns long time, I have used options like nscm=1000 ,iwrap=1 during the simulation in MD-input file. Upon finishing the simulation, I unwrap the trajectories. (It has been indicated in the manual that, unwrapping is important for calculating thediffusion properties). Then I used script (as below) to calculate the diffusion of each lipid throughout 45000 frames for all the 128 lipids I used. Finally I averaged the MSD vs time data for all the 128 lipids, and I get a plot as I attached in this mail.     ########################################################################### #!/bin/bash for i in {1..128};do system="maltoLyo12per" path="/media/glycoExtra/TRAJECTORY-chap6New/select-traj-maltoLyo12per" top="$path/$system.prmtop"  traj="md-all-maltoLyo12per-unwrap.nc" cpptraj $top << EOF trajin  $path/$traj  15001 60000 diffusion 5.0 :$i-$i diffusion-maltoLyo12per-$i.dat  average EOF done ########################################################################### My questions: 1) Is my MSD vs time plot correct? If is not than could I get some explanation what might have went wrong in my calculation? 2) There was no option given for mass weighted diffusion calculation as in the GROMACS (g_msd). But option average is given in AMBER. Does this average option represents Mass weighted MSD? Aditionally, visually I have seen the unwrapped trajectory file using VMD and I noticed the lipids remain in bilayer arrangement but the water molecules separate and go out of the box and filled vast space.  (I dont see the lipid diffuse far apart from each other). I am little worry of my data here. Could I get some explanation on the MSD plot that I got (attached here ) and possible errors might occurred if the plot is wrong? Regards Vijay 

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msd-maltoLyo12per-225ns-XY.png
(image/png attachment: msd-maltoLyo12per-225ns-XY.png)

Received on Tue Aug 19 2014 - 20:00:02 PDT
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