AMBER Archive (2005)

Subject: RE: AMBER: Error on restrained MD equilibration (AMBER 7)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 31 2005 - 11:45:19 CDT

Hi Lan,

> equilibrate the solvent. Anything else we could consider?

A few things you could try. First of all remove all the extra commas from
the last item in each namelist - some compilers don't like this. Second
specify the restraint force as 10.0 instead of 10 since it is a float. I.e.

MD heating from 0 to 300K with restraints on the solute
 &cntrl
   imin = 0, ntpr = 100, ntwx = 100, ntwe = 100, ntwr = 1000,
   nstlim =10000, dt = 0.001,
   ntb = 1,cut = 8, ntr = 1, ntc = 2, ntf = 2, nmropt = 1,
   tempi = 0.0, temp0 = 300.0, ntt = 1, tautp = 0.5
 &end
 &wt
  type='TEMP0', istep1=0, istep2=500,
                value1=0.0, value2=300.0
 &end
 &wt
  type='TEMP0', istep1=500, istep2=20000,
                value1=300.0, value2=300.0
 &end
 &wt
  type='END'
 &end
Group input for restraint atoms
10.0
RES 1 1
END
END

If that doesn't work try it out without the weight change info and see if
you can get it to work with just the restraints, as a test.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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