[gmx-users] energy-minimisation problem

SANTU BISWAS santu.biswas85 at gmail.com
Tue Jan 29 10:43:56 CET 2013

dear users,

              I am performing an energy minimization of
polypeptide(formed by 10-residues of alanine, lysine,leucine,glutamic
acid ) in vacuum box by using
Steepest Descent(initially) and then Conjugate Gradient methods in
using charmm-27 force field for all system.I saw that for lysine and
alanine potential energy
value is positive but for leucine and glutamic acid potential energy
value is nagative for both energy-
minimisation methods.
I do not understand why this is happening.

Input file for energy-minimisation is

;title                    =
cpp                     = /lib/cpp
;include               =-I../top/
define                  = -DFLEXIBLE
;         Input file

integrator             =  cg
nsteps                 =  10000
pbc                      =  no
ns_type                =  simple
nstlist                   =  0
rlist                       =  0
rcoulomb               =  0
rvdw                      =  0

;         Energy minimizing stuff

emtol                   =  0.001
emstep                 =  0.1
nstcgsteep            =  10


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