AMBER Archive (2008)

Subject: AMBER: velocity autocorrelation function for SPC felxible water model

From: Rahaman, Asif (
Date: Thu May 08 2008 - 12:07:41 CDT

Did anyone calculate velocity autocorrelation (VAC) function for SPC flexible water model? I have tried to calculate the same but I got some unusual wiggles with the function. I have taken a SPCBOX from amber and before saving the topology and coordinate file, I used to 'set default FlexibleWater on'. Then carried out some more equilibration at NPT (300K). Then collected the data with NVE simulation. Did I make any thing wrong with my simulations for calculating VAC?
My NVE input is:

 imin =0,
 ntx =5, irest =1,
 ntpr =1000, ntwe =1000, ntwx = 1000, ntwv =10, iwrap =1,
 ntr =0,
 nstlim = 500000, dt =0.001,
 ntt =0, tempi =300.0, temp0 =300.0, tautp = 0.05, vrand =999999999,
 ntc =1,
 ntf =1, ntb =1, igb =0, cut =7.0,
 nmropt =0,
I will really appreciate, if anyone send me a velocity autocorrelation for the flexible SPC water box using AMBER. and simulation protocol (input) that is used for the collecting data.
Thanks in advance.
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