AMBER Archive (2009)

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

From: Sidney Elmer (paulymer_at_gmail.com)
Date: Mon Dec 14 2009 - 19:23:50 CST

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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