AMBER Archive (1999)

Subject: gibbs+PME+PMF

From: F. Ryjacek 0313 517050 (ryjacek_at_indy.jh-inst.cas.cz)
Date: Thu Oct 21 1999 - 04:32:03 CDT

Hi all,
I'm looking for an "GIBBS expert". I tried to run gibbs free energy
simulation of two DNA bases in water TIP3P box. Both PME (IEWALD=1)
and PMF (NCORC=1) options were turned on, but results from DMW Free energy
perturbation and DMW Termodynamics integration were completely different (
59 nad 78 kcal/mol). Total simulation time was 500ps. In vacuo everything
goes O.K., the agreement between FEP and TI is about 0.1 - 0.2 kcal/mol.

Thanks for any suggestion !

F. Ryjacek
ryjacek_at_indy.jh-inst.cas.cz

Here is the input for TI :

  
TITLE: A...FT to A..THY h2o box
 &cntrl
    timlim = 9999999.0 , irest = 0 , ibelly = 0 ,
    ichdna = 0 , ipol = 0 , i3bod = 0 ,
    iewald = 1 ,
 
    ntx = 1 , ntxo = 1 , ig = 71277 ,
    tempi = 100.0000 , heat = 0.000000 ,
 
    ntb = 2 , iftres = 1 , boxx(1)= 0.000000 ,
    boxx(2)= 0.000000 , boxx(3)= 0.000000 , betar = 0.000000 ,
    ibxrd = 0 ,
 
    nrun = 1 , ntt = 5 , temp0 = 298.0000 ,
    dtemp = 999.0000 , tautp = 0.2000000 , tauts = 0.2000000 ,
    isolvp = 0 , nsel = 0 , dtuse = 0.5000000 ,
 
    ntp = 1 , npscal = 0 , pres0 = 1.000000 ,
    comp = 44.60000 , taup = 1.000000 ,
 
    ndfmin = 0 , ntcm = 0 , nscm = -1 ,
    istay = 0 , nstay = 0 , isvat = 1 ,
 
    nstlim = -1 , init = 3 , ntu = 1 ,
    t = 0.000000 , dt = 0.1000000E-02 , vlimit = 0.000000 ,
    ivemax = 0 ,
 
    ntc = 1 , ntcc = 0 , nconp = 0 ,
    tol = 0.1000000E-02 , tolr2 = 0.1000000E-01 , ncorc = 1 ,
    ishkfl = 1 , itimth = 0 , jfastw = 0 ,
 
    ntf = 1 , ntid = 0 , ntn = 3 ,
    ntnb = 1 , nsnb = 500 , idiel = 1 ,
    inbper = 0 , ielper = 0 , imgslt = 0 ,
    idsx0 = 0 , itrslu = 1 , ioleps = 0 ,
    intprt = 5 , itip = 0 ,
 
    cut = 7.00000 , scnb = 2.000000 , scee = 1.200000 ,
    dielc = 1.000000 , cut2nd = 0.000000 , cutprt = 0.000000 ,
 
    ntpr = 500 , ntwx = 500 , ntwv = 500 ,
    ntwe = 500 , ntwxm = 0 , ntwvm = 0 ,
    ntwem = 0 , ntpp = 0 , ioutfm = 0 ,
    isande = 1 , iperat = 2 , iatcmp = 1 ,
    ntatdp = 100 , icmpdr = 0 , ncmpdr = 0 ,
    ntwprt = 1000 , ntwpr0 = 0 ,
 
    ntr = 0 , nrc = 0 , ntrx = 1 ,
    taur = 0.1000000 , intr = 5 , ibigm = 1 ,
    nmrmax = 0 , iwtmax = 0 , isftrp = 0 ,
    rwell = 4.000000 ,
 
    iftime = 0 , ctimt = 40.00000 , almda = 0.000000 ,
    almdel = 0.1000000E-01 , isldyn = +2 , idifrg = 1 ,
    nstmeq = 10 , nstmul = 50 , ndmpmc = 100 ,
    idwide = 0 , ibndlm = 0 ,
 
    iavslp = 8 , iavslm = 2 , islp = 0 ,
    corrsl = 0.9500000 , amxmov = 0.1000000E-01 ,
 
    iavdel = -1 , iavdem = 2 , amxdel = 0.1000000 ,
 
    almdl0 = 0.1000000E-05 , dlmin = 0.1000000E-03 , dlmax = 0.1000000E-01 ,
    amxrst = 0.2000000 , norsts = 0 , ntsd = 0 ,
    almstp = -1.000000 ,
 
    nstpe = 100 , nstpa = 100 , dte = 0.1000000E-02 ,
    dta = 0.1000000E-02 ,
 
    ivcap = 2 , natcap = 0 , fcap = 1.500000 ,
 
 &end
 28.83319 22.127913 18.149101 90.0 90.0 90.0
 30 24 20 4 0 0 0
 0.00001
    7 11 27 29 0 0 0 1.00000 0.00000
 100.00000 180.00000 100.00000 180.00000 0 0
   12 11 27 25 0 0 0 1.00000 0.00000
 100.00000 180.00000 100.00000 180.00000 0 0
   14 12 11 27 0 0 0 1.00000 0.00000
 100.00000 180.00000 100.00000 180.00000 0 0
    6 7 11 27 0 0 0 1.00000 0.00000
 100.00000 180.00000 100.00000 180.00000 0 0
   11 27 0 0 0 0 0 1.00000 0.00000
  10.00000 2.97700 10.00000 3.65600 0 0