AMBER Archive (2008)

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

From: David A. Case (
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?


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to