AMBER Archive (2003)

Subject: gibbs calculation

From: Xiang, Tian-Xiang (txian2_at_email.uky.edu)
Date: Tue Jan 28 2003 - 13:03:44 CST

Dear Sir:

I am conducting free energy calculation for mutating a dipeptide to a monpeptide (e.g. ALA-ALA -> ALA) in a box of ~900 CCL4 using gibbs. I have the following questions:

1. As shown below (within the dashed line), the output report file shows that
14EL = 0.00, 14NB = 0.0, and BADH = 0.00 while clearly 1-4 Elec etc. are not zero. What's happen? Have I missed something? My input file is also listed below.
----------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 290.702 PRESS = 140.01
 Etotal = -382.84816 Kinetic = 4092.57320 Potential = -4475.42135
 Bond = 1118.68852 Angle = 1416.11045 Dihed = 17.30739
 1-4 VdW = 9.54944 1-4 Elec= 97.64685 Van d Waal = -6998.42849
 Elect. = -136.29551 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 771.68978 VirT = 305.16392 Volume = 154387.67267
                                                 Density = 1.55313
Current Lambda = 0.975000
 Last F.E. update: Lambda = 0.975000 Step = 2000 Method = F.E.P.
 Accumulated "forward" quantities (Regular)
    Lam+d_lam = 1.000000 F_energy = -1.64856
    ELEC = -1.273 NONB = -0.400 14NB = 0.000
    14EL = 0.000 BADH = 0.000
    EPOL = 0.000 E3bod= 0.000
 Accumulated "reverse" quantities (Regular)
    Lam-d_lam = 0.950000 F_energy = 3.29618
    ELEC = 2.484 NONB = 0.758 14NB = 0.000
    14EL = 0.000 BADH = 0.000
    EPOL = 0.000 E3bod= 0.000
------------------------------------------------------------------------------------

 gibbs input
 &cntrl
    ntb=2,
    ntt=1, tautp = 5.0,
    ntp=1,pres0=1.0,taup=1.,
    tempi=298.0,temp0=298.0,
    dt=0.001,
    nstlim=1000,
    nstmeq=300,
    nstmul=700,
    ntc=2,ntf=2,
    intprt=1,
    cut=12.,
    scnb=2.0,scee=1.2,
    ntpr=1000,
    nrun=41,
    almda=1.0,
    almdel=0.025,
    isldyn=-3,
    ielper=0,
 &end
------------------------------------------------------------------------------------
 
2. The output report file contains many lines of " nb-update: total= 912973 hbpair= 0 pert= 23698",
which is annoying. How can I supress them?

Thanks

T.-X. Xiang