[AMBER] Finding difficulty during calculation of diffusion coefficient from MSD plot

From: Sohag Biswas <cy13p1001.iith.ac.in>
Date: Sun, 29 Dec 2013 11:10:33 +0530

Dear amber users,

I need your help. I am trying to calculate diffusion coefficient of
DMF-water mixture from MSD plot. i have trajectory of 9 ns nvt. I am
calculating MSD by using this command "*diffusion mask time-step average
file_name" *. After getting MSD plot, to calculate diffusion coefficient, I
multiplied the slope by 10/6, which is given in Amber 13 tools. Now when i
am changing time-step, my diffusion coefficient value also changes. I
started calculation MSD by taking time-step 20 (*dt*ntwx*) to 1. So, I want
to know that how to choose time-step and what will be unit? Please somebody
helps me to solve this problem. Here, I have given my md.in input.

 Equil MD
 imin=0, irest=0, ntx=1,
 nstlim=4500000, dt=0.002,
 ntt=3, temp0=293.15, ig=-1, tautp=5.0,
 ntp=0, ntb=1,
 ntf=2, ntc=2, tol=0.0000001,
 cut=8.0, nsnb=1,
 ntpr=1000, ntwr=10000, ntwx=10000, ntwe=10000, ntwv=-1,
 nfft1=40, nfft2=40, nfft3=40,

Sohag Biswas
IIT Hyderabad, India
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Received on Sat Dec 28 2013 - 22:00:02 PST
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