PMF

From: X. Tan <xjtan.u.washington.edu>
Date: Wed, 2 Jul 2003 12:02:53 -0700 (PDT)

Dear amber users,

I have a question about PMF calculation. Basically, I have performed a PMF
calculation on two torsion angles with Gibbs, and wanted 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 were something 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?

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

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