AMBER: Short trajectory segments / frequent restarts causes explosion

From: David Cerutti <>
Date: Thu, 17 Apr 2008 14:04:14 -0700 (PDT)


    This is very bothersome. I now have three examples of using short
trajectory segments (2000 to 10000 steps at 1.5fs timestep) causes the
system to begin to fall apart and eventually blow up.
    The first came a couple of months ago, when I was trying to submit jobs
more frequently so I could work around a novice user who was also trying
to use the system (in the absence of a queue, I had a check before each
submission to see whether he had started something). I switched from
100,000 steps per run to 2,000. Immediately, things started to go
slightly off. With each restart, it was as if the system was being
slightly kicked out of its normal, happy state. The increase in RMSD was
rather exponential, and in a few nanoseconds it maxed out at around 40A,
with the protein completely unfolded. I went back to the original 100,000
steps per segment and restarted from the last good set of coordinates and
everything's been fine for tens of nanoseconds since.
    The next two examples came today when I was simulating different but
related systems. I switched from 1,000,000 steps per leg to 10,000 to try
and make better headway through a supercomputer queue with shorter jobs.
Both systems showed immediate and steady increases in RMSD, one of them
much too high to be a normal continuation of the original trajectory. I
expect that these increases would become exponential, but I'm not going to
wait to find out. The first example was using the netcdf coordinate
output, the second two used .crd format, but the restart file was written
in the %12.7f%12.7f%12.7f%12.7f%12.7f%12.7f format in all cases.
    Below is the input file I was using (the parameters are the same across
all three runs, save for the coordinate output format as I just mentioned.
I can't see how the more frequent restarts would really drive the system
so far out of whack, given the degree of precision in the restart file.
It makes me wonder, though, if something is going wrong with every restart
of my system, and if it's just healing within 100,000 or 1,000,000 steps
so that it's not as apparent.



Molecular dynamics at a slightly improved rate

   nmropt = 0,
   ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
   ntpr = 100, ntwx = 1000, ntwv = 0, ntwe = 100,
   iwrap = 1, ioutfm = 1,

   ntf = 2, ntb = 2,
   cut = 9.0,

   ibelly = 0, ntr = 0,

   imin = 0,
   nstlim = 1000000,
   nscm = 1000,
   t = 0.0, dt = 0.0015,

   temp0 = 293.0, tempi = 293.0,
   ig = 982742,
   ntt = 3,
   gamma_ln = 3.0,
   vlimit = 20.0,

   ntp = 1, pres0 = 1.0, comp = 44.6,
   taup = 1.0,

   ntc = 2, tol = 0.00001, watnam = 'WAT ',

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:20:09 PDT
Custom Search