AMBER Archive (2007)

Subject: AMBER: Problem with Getting SHAKE to work

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Sat Sep 15 2007 - 13:04:14 CDT


Hello,

    I was under the impression that all I had to do to turn on SHAKE in a
pmemd dynamics run was set ntf = 2 and ntc = 2; however, when I do this I
find that bonds containing hydrogen are still fluctuating. This creates
problems, of course, when polar hydrogens come too near a negatively
charged atom and cause the simulation to crash.

    Here is my input file. Can anyone suggest a remedy?

>>>>>
Round 1 of MD equilibration
  &cntrl

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

   ntf = 2, ntb = 1,
   cut = 9.0,

   ibelly = 1, ntr = 0,

   imin = 0,
   nstlim = 100000,
   nscm = 1000,
   t = 0.0, dt = 0.0005,

   temp0 = 293.0, tempi = 0.0,
   ig = 9376841,
   ntt = 3,
   gamma_ln = 3.0,
   vlimit = 20.0,

   ntp = 0, pres0 = 1.0, comp = 44.6,
   taup = 1.0,

   ntc = 2, tol = 0.001, watnam = 'WAT ',

  &end
Group input for restraint mask
FIND
SEARCH
ATOM 1 29008
END
END
<<<<<

Thanks!

Dave
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