AMBER Archive (2008)

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

From: Rahaman, Asif (asif-rahaman_at_uiowa.edu)
Date: Thu May 08 2008 - 15:42:22 CDT

Dear Prof. Case,
 
Yes, I did include the frcmod.spcfw file while creating the topology and crd file. I do not understand why I get some wiggles at the bottom of the VAC function. Is it something inherent in AMBER SPC flexible water model or something is wrong with my simulations. Has the model been tested in terms of VAC?
 
I am including some values for the VAC that I get - Is it reasonable (the wiggles at the bottom)? The following data shows the wiggles around .5ps.
 
Thank you very much for your reply.
  
 
   Time(ps) VAC
 
 0.0000000E+00 1.000000
  9.9999998E-03 0.8559352
  2.0000000E-02 0.6650298
  2.9999999E-02 0.4163236
  3.9999999E-02 0.2313780
  4.9999997E-02 8.4128335E-02
  5.9999999E-02 -1.7332524E-02
  7.0000000E-02 -1.5057207E-02
  7.9999998E-02 -1.8866528E-02
  8.9999996E-02 3.6743239E-02
  9.9999994E-02 3.5760358E-02
  0.1100000 5.8635738E-02
  0.1200000 3.3301745E-02
  0.1300000 1.8220371E-02
  0.1400000 5.1823854E-03
  0.1500000 -1.3002072E-02
  0.1600000 -1.6188810E-02
  0.1700000 -4.5868881E-02
  0.1800000 -5.8757056E-02
  0.1900000 -9.7693942E-02
  0.2000000 -0.1155176
  0.2100000 -0.1315789
  0.2200000 -0.1257085
  0.2300000 -0.1087348
  0.2400000 -9.2228755E-02
  0.2500000 -7.7798687E-02
  0.2600000 -8.6392239E-02
  0.2700000 -0.1026760
  0.2800000 -0.1291634
  0.2900000 -0.1453908
  0.3000000 -0.1478464
  0.3100000 -0.1323189
  0.3200000 -0.1034212
  0.3300000 -7.5439863E-02
  0.3400000 -5.6037687E-02
  0.3500000 -5.3187046E-02
  0.3600000 -6.2901497E-02
  0.3700000 -7.6417178E-02
  0.3800000 -8.5140683E-02
  0.3900000 -7.9733431E-02
  0.4000000 -6.4069301E-02
  0.4100000 -4.0927175E-02
  0.4200000 -2.1696510E-02
  0.4300000 -1.1715076E-02
  0.4400000 -1.3313307E-02
  0.4500000 -2.3511166E-02
  0.4600000 -3.2459456E-02
  0.4700000 -3.5860125E-02
  0.4800000 -2.8022839E-02
  0.4900000 -1.4729873E-02
  0.5000000 2.6188302E-04
  0.5100000 9.2854071E-03
  0.5200000 9.6649462E-03
  0.5300000 2.2617057E-03
  0.5400000 -8.3379177E-03
  0.5500000 -1.5220666E-02
  0.5600000 -1.5844202E-02
  0.5700000 -9.1658123E-03
  0.5800000 7.9418649E-04
  0.5900000 9.7526181E-03
  0.6000000 1.2789473E-02
  0.6100000 8.9718997E-03
  0.6200000 -1.3336645E-04
  0.6300000 -9.7939614E-03
  0.6400000 -1.6244598E-02
  0.6500000 -1.6772110E-02
  0.6600000 -1.2718561E-02
  0.6700000 -6.8835048E-03
  0.6800000 -1.8771846E-03
  0.6900000 4.3068645E-05
  0.7000000 -7.9941784E-04
  0.7100000 -4.2776600E-03
  0.7200000 -7.2688586E-03
  0.7300000 -9.2826411E-03
  0.7400000 -9.3777943E-03
  0.7500000 -8.9031449E-03
  0.7600000 -8.2996218E-03
  0.7700000 -7.6302355E-03
  0.7800000 -7.3541170E-03
  0.7900000 -6.3178730E-03
  0.8000000 -4.9640876E-03
  0.8100000 -2.2924880E-03
  0.8200000 2.0105342E-04

________________________________

From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Thu 5/8/2008 1:00 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: velocity autocorrelation function for SPC felxible water model

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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