AMBER Archive (2004)

Subject: AMBER: About the free energy difference in vacuum with GIBBS.

From: Chunhu Tan (tanc_at_uci.edu)
Date: Mon Jul 12 2004 - 17:34:35 CDT

Hi, All,

I am sorry to post such a trivial question again, but I really do not know what's wrong with my simulation....
I want to calculate the free energy difference between H3C-SH and H3C-OH in vacuum. With xleap, I built two sets of .pert_top and .inpcrd files: H3C-SH -> H3C-OH and reverse, and then minimized and equilibrated them with the same input files. After that, I GIBBS them with also the same input file.(All input files as shown below). As I thought, the results of this two simulations will be almost the same except the sign, but my results were entirely different. Who can tell me, what's wrong with my calculation?
Any suggestion or answer will be appreciated!

 Informations related:
1) Perturbation: atom: S , type : SH, charge: -0.3119 ----> atom: O, type: OH, charge: -0.6546
                          atom: H, tpye : HS, charge: 0.1933 ----> atom: H, type: HO, charge: 0.4275

2) Input files:
    (a) Minimization:
         &cntrl
             imin=1,
             nstlim=1000, maxcyc=1000, ncyc=1000,
             ntpr=100, ntwr=1000,
             cut=999.,
             ntb=0
           /
    (b) Equilibration:
          &cntrl
             imin = 0, ntb = 0, nscm =50,
             igb = 0, ntpr = 100, ntwx = 0,
             ntt = 1,
             tempi = 300.0, temp0 = 300.0,
             nstlim = 100000, dt = 0.0005,
            cut = 999
           /
   (c) Gibbs:
         &cntrl
            irest=0, ntx=5, init=4,
            nstlim=-1, dt=0.0005,
            nscm=100,
            ntt= 1,
            tol=0.000005,
            ntb=0, temp0=300.0,
            idiel=0, scee=1.2,
            idifrg=1, isldyn=-3,almda=1,isande=1,
            nstmeq=10000, nstmul=200000,
            ntpr=100000
         &end

3) The result of H3C-SH ->H3C-OH:

      A V E R A G E S O V E R 2310000 S T E P S
          
 NSTEP = 2310000 TIME(PS) = 1155.000 TEMP(K) = 300.274 PRESS = 0.00
 Etotal = 11.20216 Kinetic = 3.58022 Potential = 7.62194
 Bond = 0.43629 Angle = 3.14981 Dihed = 0.06287
 1-4 VdW = -0.00218 1-4 Elec= 3.97515 Van d Waal = 0.00000
 Elect. = 0.00000 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000

      R M S F L U C T U A T I O N S
        
 NSTEP = 2310000 TIME(PS) = 1155.000 TEMP(K) = 23.118 PRESS = 0.00
 Etotal = 1.64080 Kinetic = 0.27564 Potential = 1.66274
 Bond = 0.35785 Angle = 0.44597 Dihed = 0.05335
 1-4 VdW = 0.00197 1-4 Elec= 1.61120 Van d Waal = 0.00000
 Elect. = 0.00000 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000

 Current Lambda = 0.000000
 Last F.E. update: Lambda = 0.000000 Step = 2310000 Method = T.I.
 Accumulated "forward" quantities (Regular)
    Lambda = 0.000000 F_energy = -4.60629
    Enthalpy = -4.71059 T*Entropy = -0.10430
    ELEC = 0.000 NONB = 0.000 14NB = -0.007
    14EL = -4.062 BADH = -0.537
 Quantities used in integration:
    <dV/d_lam> = -5.7997839 <V(lam-dep.)> = 15.976468
    <V(lam-indep.)> = -5.5413843 <V(lam-dep)*dV/d_lam> = -93.460111
    <V(lam-indep)*dV/d_lam> = 33.021013
 ------------------------------------------------------------------------------

4) The result of H3C-OH -> H3C-SH:

      A V E R A G E S O V E R 2310000 S T E P S

 NSTEP = 2310000 TIME(PS) = 1155.000 TEMP(K) = 300.212 PRESS = 0.00
 Etotal = 7.49246 Kinetic = 3.57947 Potential = 3.91299
 Bond = 0.27657 Angle = 3.26674 Dihed = 0.04981
 1-4 VdW = -0.00228 1-4 Elec= 0.32216 Van d Waal = 0.00000
 Elect. = 0.00000 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000

      R M S F L U C T U A T I O N S

 NSTEP = 2310000 TIME(PS) = 1155.000 TEMP(K) = 15.301 PRESS = 0.00
 Etotal = 0.03915 Kinetic = 0.18243 Potential = 0.18638
 Bond = 0.43608 Angle = 0.47493 Dihed = 0.05323
 1-4 VdW = 0.00199 1-4 Elec= 0.01347 Van d Waal = 0.00000
 Elect. = 0.00000 H-bond = 0.00000 Constraint = 0.00000
 Ekcmt = 0.00000 VirT = 0.00000 Volume = 0.00000

 Current Lambda = 0.000000
 Last F.E. update: Lambda = 0.000000 Step = 2310000 Method = T.I.
 Accumulated "forward" quantities (Regular)
    Lambda = 0.000000 F_energy = -0.07594
    Enthalpy = -0.02845 T*Entropy = 0.04749
    ELEC = 0.000 NONB = 0.000 14NB = 0.008
    14EL = -0.120 BADH = 0.036
 Quantities used in integration:
    <dV/d_lam> = -0.62511886E-01 <V(lam-dep.)> = 1.9411751
    <V(lam-indep.)> = 1.9825166 <V(lam-dep)*dV/d_lam> = -0.13071458
    <V(lam-indep)*dV/d_lam> = -0.10713941
 ------------------------------------------------------------------------------

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