AMBER Archive (2009)

Subject: [AMBER] Gap in rst file

From: Katrina Lexa (klexa_at_umich.edu)
Date: Mon Sep 28 2009 - 09:47:43 CDT

Hello,
I know what it means to get **** in my rst file, but a couple of my
recent runs have large gaps in the rst file and there's nothing in the
.out or via visualization to suggest a problem with the system that I
restarted from.
Is this gap just an energetics problem? The only other solution, aside
from just restarting, that I could find on the amber archive is from
Ross Walker back in 2006 to write out binary files from now on. I used
ntxo = 0 to get unformatted output and ntx = 5 for the first run, and
expected that I could read in the output with ntx = 6 and ntrx = 0. But
when I do that, I get an error unit -5, internal formatted read.
Any advice would be appreciated,
Thank you
Katrina Lexa

1st Production run
 &cntrl
  ntwe = 1000, ntwx = 1000, ntwr = 1000, ntpr = 1000, ntwv = 25000,
  ntt = 1, temp0 = 310.0, tempi = 310.0,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 10.0,
  ntb = 2, ntp = 1, ntc = 2, ntf = 2,
  nstlim = 200000, dt = 0.0020,
  igb = 0,
  imin = 0, irest = 1, ntxo = 0, ntx = 5,
  ig = 2881,
 /
 
2nd Production run
 &cntrl
  ntwe = 1000, ntwx = 1000, ntwr = 1000, ntpr = 1000, ntwv = 25000,
  ntt = 1, temp0 = 310.0, tempi = 310.0,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 10.0,
  ntb = 2, ntp = 1, ntc = 2, ntf = 2,
  nstlim = 2000000, dt = 0.0020,
  igb = 0,
  imin = 0, irest = 1, ntrx = 0, ntxo = 0, ntx = 6,
  ig = 2881,
 /

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