AMBER Archive (2003)

Subject: AMBER: PMF

From: X. Tan (xjtan_at_u.washington.edu)
Date: Tue Jul 15 2003 - 12:02:47 CDT

Dear amber users,

A week ago, I sent this email to the list, but there is no response. So I
would like to send it again in case there are some people who did not see it.

I have a question about PMF calculation. Basically, I have performed a PMF
calculation on two torsion angles with Gibbs, and I'd like to want to
know how large the energy penalty would be for this conformational change.
We expected to see a large value, but the calculated free energy is pretty
small. In my output file, we found there was something which looks really
suspicious: All the energy terms are zero except CORC...

    ELEC = 0.000 NONB = 0.000 14NB = 0.000
    14EL = 0.000 BADH = 0.000 CORC = 0.108
    EPOL = 0.000 E3bod= 0.000

  Constrained Internals at Last F.E. Update Lam L+d_L
L-d_L
 H1 (3352)-C1 (3351)-O1 (3353)-C7 (3354) -27.3650 -26.4000
-28.3300
 C1 (3351)-O1 (3353)-C7 (3354)-C8 (3355) -123.7200 -125.0000
-122.4400

Could anyone tell me what has gone wrong with my calculation? Why
ELEC, NONB, 14NB... are all Zero? Thanks for your attention. Any
suggestion would be greatly appreciated!

-----------------------------------------
Here is my input file:

 &cntrl
    timlim = 0.1000000E+09 , irest = 1 , ibelly = 0
,
    ichdna = 0 , ipol = 0 , i3bod = 0
,
    iewald = 0 ,

    ntx = 7 , ntxo = 1 , ig = 71277
,
    tempi = 10.0000 , heat = 0.0000000E+00 ,

    ntb = 2 , 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 = 999.0000 , tautp = 0.5000000 , tauts = 0.5000000
,
    isolvp = 0 , nsel = 0 , dtuse = 0.5000000
,

    ntp = 1 , npscal = 0 , pres0 = 1.000000
,
    comp = 44.60000 , taup = 0.2000000 ,

    ndfmin = 0 , ntcm = 0 , nscm = -1
,
    istay = 0 , nstay = 0 , isvat = 1
,

    nstlim = 25000 , init = 4 , ntu = 1
,
    t = 0.0000000E+00 , dt = 0.1000000E-02 , vlimit = 20.00000
,
    ivemax = 0 ,

    ntc = 3 , ntcc = 0 , nconp = 0
,
    tol = 0.1000000E-07 , tolr2 = 0.1000000E-03 , ncorc = 1
,
    ishkfl = 6 , itimth = 0 , jfastw = 0
,

    ntf = 3 , ntid = 0 , ntn = 3
,
    ntnb = 1 , nsnb = 25 , idiel = 1
,
    inbper = 0 , ielper = 0 , imgslt = 0
,
    idsx0 = 400 , itrslu = 1 , ioleps = 0
,
    intprt = 5 , itip = 0 ,

    cut = 10.00000 , scnb = 2.000000 , scee = 1.200000
,
    dielc = 1.000000 , cut2nd = 0.0000000E+00 , cutprt =
0.0000000E+00 ,

    ntpr = 500000 , 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 = -1 , ntwpr0 = 0 ,

    ntr = 0 , nrc = 0 , ntrx = 1
,
    taur = 0.1000000 , intr = 2 , ibigm = 0
,
    nmrmax = 0 , iwtmax = 0 , isftrp = 0
,
    rwell = 4.000000 ,

    iftime = 0 , ctimt = 40.00000 , almda = 1.000000
,
    almdel = 0.5000000E-01 , isldyn = -3 , idifrg = 0
,
    nstmeq = 10000 , nstmul = 15000 , ndmpmc = 0
,
    idwide = 1 , 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 = 10000 , nstpa = 15000 , dte =
0.1000000E-02 ,
    dta = 0.1000000E-02 ,

    ivcap = 2 , natcap = 0 , fcap = 1.500000
,

 &end
 3352 3351 3353 3354 0 1 2 1.00000 0.00000
   0.00000 -26.40000 0.00000 -45.70000 0 0
 3351 3353 3354 3355 0 1 2 1.00000 0.00000
   0.00000-125.00000 0.00000 -99.40000 0 0

-------------------------------------------------

Thanks in advance.

Xiaojian Tan

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