AMBER Archive (2003)

Subject: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks.

From: Christophe L M J Verlinde (verlinde_at_u.washington.edu)
Date: Tue Sep 02 2003 - 12:57:52 CDT


Dear AMBER users,

We are trying to perform PMF calculations with umbrella sampling
in GIBBS, but we must be doing something wrong because the
reported free energy difference is always ZERO. Even when we
tried a very simple test system, changing ethane from the
staggered to the ecclipsed conformation, the result was zero.

PLEASE, CAN SOMEONE GIVE US A CLUE ON HOW TO CORRECT THE INPUT FOR
THIS SIMPLE PMF CALCULATION. From the manual it is not clear why and
how RKEQ2 is needed to drive just 1 torsion angle. Any
help will be greatly appreciated.

Christophe Verlinde
-------------------------------------------------------------------------------
Here we go for changing ethane from the staggered to the ecclipsed
conformation (Defaults are also included for completeness):
(most likely we mess up in the last 2 lines?)

    H(2) H(6)
     \ /
(3)H- C(1)-C(5)-H(7)
     / \
    H(4) H(8)

    timlim = 0.1000000E+09 , irest = 0 , ibelly = 0 ,
    ichdna = 0 , ipol = 0 , i3bod = 0 ,
    iewald = 0 ,
 
    ntx = 5 , ntxo = 1 , ig = 71277 ,
    tempi = 10.0000 , heat = 0.0000000E+00 ,
 
    ntb = 0 , iftres = 0 , boxx(1)= 0.0000000E+00 ,
    boxx(2)= 0.0000000E+00 , boxx(3)= 0.0000000E+00 , betar = 0.0000000E+00 ,
    ibxrd = 0 ,
 
    nrun = 21 , ntt = 5 , temp0 = 298.0000 ,
    dtemp = 0.0000 , tautp = 0.2000000 , tauts = 0.2000000 ,
    isolvp = 0 , nsel = 0 , dtuse = 0.5000000 ,
 
 
    ndfmin = 0 , ntcm = 0 , nscm = -1 ,
    istay = 0 , nstay = 0 , isvat = 1 ,
 
    nstlim = 100000 , init = 4 , ntu = 1 ,
    t = 0.0000000E+00 , dt = 0.5000000E-03 , vlimit = 20.00000 ,
    ivemax = 0 ,
 
    ntc = 3 , ntcc = 0 , nconp = 0 ,
    tol = 0.1000000E-07 , tolr2 = 0.1000000E-03 , ncorc = 1 ,
 
    ntf = 3 , ntid = 0 , ntn = 3 ,
    ntnb = 1 , nsnb = 99999 , idiel = 1 ,
    inbper = 0 , ielper = 0 , imgslt = 0 ,
    idsx0 = 400 , itrslu = 1 , ioleps = 0 ,
    intprt = 5 , itip = 0 ,
 
    cut = 20.0000 , scnb = 2.000000 , scee = 1.200000 ,
    dielc = 1.000000 , cut2nd = 0.0000000E+00 , cutprt = 0.0000000E+00 ,
 
    ntpr = 200000 , ntwx = -1 , ntwv = -1 ,
    ntwe = -1 , ntwxm = 0 , ntwvm = 0 ,
    ntwem = 0 , ntpp = 0 , ioutfm = 0 ,
    isande = 1 , iperat = 0 , iatcmp = 0 ,
    ntatdp = 0 , icmpdr = 0 , ncmpdr = 0 ,
    ntwprt = 0 , ntwpr0 = 0 ,
 
    ntr = 0 , nrc = 0 , ntrx = 1 ,
    taur = 0.1000000 , intr = 1 , ibigm = 0 ,
    nmrmax = 0 , iwtmax = 0 , isftrp = 0 ,
    rwell = 4.000000 ,
 
    iftime = 0 , ctimt = 40.00000 , almda = 1.000000 ,
    almdel = 0.50000E-01 , isldyn = -3 , idifrg = 0 ,
    nstmeq = 30000 , nstmul = 70000 , ndmpmc = 0 ,
    idwide = 0 , ibndlm = 0 ,
 
    iavslp = 8 , iavslm = 2 , islp = 0 ,
    corrsl = 0.8000000 , amxmov = 0.1000000E-01 ,
 
    iavdel = -1 , iavdem = 2 , amxdel = 0.1000000 ,
 
    almdl0 = 0.100000E-02 , dlmin = 0.1000000E-04 , dlmax = 0.1000000E-01 ,
    amxrst = 0.9999999E-01 , norsts = 0 , ntsd = 0 ,
    almstp = -1.000000 ,
 
    nstpe = 30000 , nstpa = 70000 , dte = 0.1000000E-02 ,
    dta = 0.1000000E-02 ,
 
    ivcap = 2 , natcap = 0 , fcap = 1.500000 ,
 
 &end
    2 1 5 6 1 1 0 1.00000 0.00000
   5.00000 60.00000 5.00000 0.00000 0 0

Christophe L.M.J. Verlinde, Ph.D.

Biomolecular Structure Center
University of Washington - Box 357742
Health Sciences Building K-428A
1959 NE Pacific Ave
Seattle, WA 98195
T:(206)543-8865 F:(206)685-7002
URL: www.bmsc.washington.edu/people/verlinde

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