AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu May 08 2008 - 13:00:28 CDT

On Thu, May 08, 2008, Rahaman, Asif wrote:
>
> 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?

Did you include the frcmod.spcfw file when you set up the system?

...dac

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