[AMBER] Behavior of MSD at different collision frequency values

From: Abdullah Bin Faheem <abdullahbinfaheem.hotmail.com>
Date: Mon, 11 Feb 2019 10:13:07 +0000

Dear all,

I would like to inquire about some behaviour observed while running NPT simulations on electrolyte systems by both using single long trajectoriesor dividing the long trajectory into numerous smaller runs (for e.g. one 1.5 ns run or three 500 ps runs). It seems that at each restart the MSD curve shows a "bump", where the MSD curve drops in slope at the end. Reducing the collision frequency (gamma_ln) from 5 ps to 1 ps (for Langevin dynamics at ntt=3), seems to give more similar MSD curves however the drop in slope exists. This drop only exists for the aforementioned smaller runs. I have attached both MSD's for reference and the input file is as follows:

NPT ensemble simulation with temperature scaling
  imin = 0, irest = 1, ntx = 5, ntpr = 500, ntave = 1000,
  ntwr = 500, ntwx = 100, ntwe = 50, ntf = 2, ntc = 2, ntb = 2,
  cut = 12.0, nsnb = 10, nstlim = 500000, dt = 0.001,
  tempi = 298.0, temp0 = 298.0, ntt = 3, tautp = 1.0,
  ntp = 1, pres0 = 1.0, taup = 1.0, ioutfm=1, gamma_ln=5,

Is the behaviour of the MSD curves dependent on the value of the collision frequency, if so, then in what way? And has anyone experianced similar behaviour regarding a drop in the MSD slope, at the end of each run before? Also is there a specific reason as to why their exists a greater difference in MSD curves at higher collision frequency values?


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MSD at collision frequency of 1.png
(image/png attachment: MSD_at_collision_frequency_of_1.png)

MSD at collision frequency of 5.png
(image/png attachment: MSD_at_collision_frequency_of_5.png)

Received on Mon Feb 11 2019 - 02:30:02 PST
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