# gibbs calculation

From: Xiang, Tian-Xiang <txian2_at_email.uky.edu>
Date: Tue 28 Jan 2003 14:03:44 -0500

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
Received on Tue Jan 28 2003 - 11:03:44 PST
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