sander VS sander_classic

From: Khatcharin Siriwong <siriwong_at_theochem.tu-muenchen.de>
Date: Thu 08 Mar 2001 19:18:44 +0100

Dear All,

I have run MD using SANDER_CLASSIC with input;
-------------------
equil_step 1 dynamics step 1, 25 kcal/mol.A solute restraint
 &cntrl
  ntx = 1, irest = 0, nmrmax = 0,

  imin = 0,
  maxcyc = 1000, ncyc = 5000,
  ntmin = 1, dx0 = 0.01, dxm = 0.5, drms = 0.0001,

  nrun = 1,
  nstlim = 30,
  dt = 0.002, init = 3, t = 0.0,
  timlim = 999999., ndfmin = 0, ntcm = 0, nscm = 0,

  ntpr = 10, ntwr = 30,
  ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,

  cut = 9.0, ntnb = 1, nsnb = 10, ntid = 0,
  scnb = 2.0, scee = 1.2, cut2nd = 0.0, ichdna = 0,
  idiel = 1, dielc = 1.0,

  ntb = 2, ntp = 1, npscal = 1,
  pres0 = 1.0, comp = 44.6, taup = 0.2,

  ntc = 2, tol = 0.0005,
  ntf = 2,

  ibelly = 0, ntr = 1,

  temp0 = 300.0, tempi = 300.0,
  ig = 71277, heat = 0.0,
  ntt = 1, isolvp = 0, dtemp = 0.0,
  tautp = 0.2, tauts = 0.2, vlimit = 20.0,
  tauv0 = 0.0, tauv = 0.1, vzero = 0.0,

  isftrp = 0, rwell = 0.0,

  ipol = 0,

  imgslt = 0, iftres = 1,
  jfastw = 0,

  ivcap = 0, matcap = 0, fcap = 1.5,

  iewald = 1,

 &end
46.2573613 45.0369329 57.8298522 90.0000000 90.0000000 90.0000000
48 48 60 4 0 0 0
0.00001
Constraints
25.0
RES 1 20
END
END
=======================

and I tried to modify this input to run with SANDER by deleting some
variables
which were not defined in SANDER, as following

----------
equil_step 1 dynamics step 1, 25 kcal/mol.A solute restraint
 &cntrl
  ntx = 1, irest = 0, nmropt = 0,

  imin = 0,
  maxcyc = 1000, ncyc = 5000,
  ntmin = 1, dx0 = 0.01, dxm = 0.5, drms = 0.0001,

  nstlim = 30,
  dt = 0.002, t = 0.0,
  timlim = 999999., ndfmin = 0, ntcm = 0, nscm = 0,

  ntpr = 10, ntwr = 30,
  ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,

  cut = 9.0, nsnb = 10,
  scnb = 2.0, scee = 1.2,
                    dielc = 1.0,

  ntb = 2, ntp = 1, npscal = 1,
  pres0 = 1.0, comp = 44.6, taup = 0.2,

  ntc = 2, tol = 0.0005,
  ntf = 2,

  ibelly = 0, ntr = 1,

  temp0 = 300.0, tempi = 300.0,
  ig = 71277, heat = 0.0,
  ntt = 1, dtemp = 0.0,
  tautp = 0.2, vlimit = 20.0,

  ipol = 0,

  jfastw = 0,

  ivcap = 0, matcap = 0, fcap = 1.5,

  igb = 0, gbparm = 2, readrad = 0,
  offset = 0.09, igbfreq= 1, gbsa = 0,
  surften= 0.005,

 &end

 &ewald
   a = 46.2573613, b = 45.0369329, c = 57.8298522,
   alpha = 90.000, beta = 90.000, gamma = 90.000,
   nfft1 = 48, nfft2 = 48, nfft3 = 60,
   order = 4, dsum_tol = 0.00001,
 &end
Constraints
25.0
RES 1 20
END
END
======================

I obtained the SANDER result which quite different from SANDER_CLASSIC
result and
running SANDER toke cpu time more than running SANDER_CLASSIC.

Could anyone help me to modify input for SANDER to obtain the
corresponding result with SANDER_CLASSIC?

Thank you very much.

Sincerely yours,
Khatcharin
Received on Thu Mar 08 2001 - 10:18:44 PST
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