[gmx-users] energy-mimisation-problem

SANTU BISWAS santu.biswas85 at gmail.com
Wed Jan 9 18:20:13 CET 2013

dear users,

              I am performing an energy minimization of
apolypeptide(formed by alanine-10-residues) in vacuum box by using
Steepest Descent(initially) and then Conjugate Gradient methods in
gromacs_4.5.5_doubleprecision.The chain length of
alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range
interactions.so i use cutoff 2.0 nm .But in the
output (.log )file there is a contribution of energy for long-range
interactions(in both energy minimisation methods).
I do not understand why this is happening.

the input file for energy minimisation is,

;title                    =
cpp                      = /lib/cpp
;include                  =-I../top/
define                   = -DFLEXIBLE
;         Input file
integrator              =  steep/cg
nsteps                  =  10000
nstlist                 =  1
rlist                   =  1.0
rcoulomb                =  2.0
rvdw                    =  2.0
;         Energy minimizing stuff
emtol                   =  0.001
emstep                  =  0.1
nstcgsteep              =  10

the output(.log )file is,

 Energies (kJ/mol)
           Bond          Angle            Proper Dih.
Ryckaert-Bell.          LJ-14
    8.48244e+00    2.10205e+01    2.39409e+00           9.86941e+01
     Coulomb-14        LJ (SR)        LJ (LR)          Coulomb (SR)
Coulomb (LR)
    1.63221e+03   -1.64038e+02   -4.97232e-01   -3.00455e+03   -1.00138e+01
      Potential       Pressure (bar)
   -1.26841e+03    0.00000e+00


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