AMBER Archive (2008)Subject: AMBER: velocity autocorrelation function for SPC felxible water model
From: Rahaman, Asif (asifrahaman_at_uiowa.edu)
Date: Thu May 08 2008  12:07:41 CDT
Hi,
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:

&cntrl
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,
&end

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.

The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
