AMBER Archive (2009)

Subject: Re: [AMBER] comparing coordinates from restart file and ptraj outputs

From: Jason Swails (jason.swails_at_gmail.com)
Date: Mon Dec 14 2009 - 19:53:39 CST

This is to be expected, as the restart file is 1 step ahead of the
final mdcrd I believe. You can check this by rerunning exactly the
same calculation for N steps, and compare that to the N+1th frame of
the mdcrd from your first simulation. It may not match exactly due to
the fact that the precision of a restart is different than a mdcrd,
but it should match to the precision of the mdcrd.

Hope this helps,
Jason

On Mon, Dec 14, 2009 at 8:23 PM, Sidney Elmer <paulymer_at_gmail.com> wrote:
> Hi,
>
> I am getting inconsistencies when comparing the coordinates from the restart
> file generated by sander and the output files generated from ptraj.  See
> below for a summary of what I did.  Is this a bug or am I missing
> something?  Thanks for any insights.
>
> Sid
>
> 1. setup a run with 500 steps; restart file updated every 100 steps:
> $ cat mdin
>  &cntrl
>  nstlim = 500, dt = 0.002,
>  ntx = 5, irest = 1,
>  ntf = 2, ntc = 2,
>  ntt = 3, temp0 = 310.0, gamma_ln = 5.0,
>  ntb = 2, ntp = 1, pres0 = 1.0,
>  ntwx = 1, ntwr = 100, ntpr = 1,
>  /
>
> 2. execute run:
> $ sander -O
>
> 3. thus, after execution finishes, the coordinates in "restrt" file should
> match coordinates from frame 500, correct?  To test this, I dumped the
> contents of "mdcrd" into separate files for each frame:
> $ cat ptraj.cmd
> trajin mdcrd
> trajout out.restrt restart
>
> $ ptraj prmtop < ptraj.cmd
>
> 4. compare coordinates from "restrt" file with the coordinates from frame
> 500:
> $ head restrt out.restrt.500
> ==> restrt <==
>
>
> 12229
>  36.3305038  13.8660564  76.3226335  36.8364002  13.4737666  77.1038361
>  35.6825593  13.1233185  76.1021414  35.8160375  14.7061467  76.5455088
>  37.2998211  13.9844329  75.2107251  37.9789653  13.1328655  75.2519122
>  36.6052142  13.9179318  73.8372047  35.9462419  13.0519369  73.7746877
>  36.0497970  14.8077383  73.5407853  37.4626397  13.7198942  72.5764882
>  38.1500466  12.8983887  72.7782423  36.8921438  13.5181536  71.6698818
>  38.6032029  15.1222338  72.0682800  38.9906380  14.4044642  70.4856256
>  38.0884652  14.4689332  69.8773264  39.6575401  15.1439896  70.0424002
>
> ==> out.restrt.500 <==
> trajectory generated by ptraj
> 12229
>  36.3300018  13.8699999  76.3199997  36.8400002  13.4700003  77.0999985
>  35.6800003  13.1199999  76.0999985  35.8199997  14.7100000  76.5500031
>  37.2999992  13.9799995  75.2099991  37.9799995  13.1300001  75.2500000
>  36.6100006  13.9200001  73.8399963  35.9500008  13.0500002  73.7699966
>  36.0499992  14.8100004  73.5400009  37.4599991  13.7200003  72.5800018
>  38.1500015  12.8999996  72.7799988  36.8899994  13.5200005  71.6699982
>  38.5999985  15.1199999  72.0699997  38.9900017  14.3999996  70.4899979
>  38.0900002  14.4700003  69.8799973  39.6599998  15.1400003  70.0400009
>
> 5. I then wrote a script that calculated the difference between each element
> in the coordinate vectors to see if there was a systematic change in the
> coordinates; the differences are random distributed between -0.005 and
> +0.005, which are not negligible differences.
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> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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