[gmx-users] Energy minimization result problem

[neha_bharty]

Hello
I am new user of gromacs. I am using gromacs 4.6.3
I wanted to minimize the energy of a protein. Before energy minimization the
prockeck result for Ramachandran plot was 89% in allowed region but after
energy minimization the result become worse i.e. 87%.
I was performing energy minimization to refine the model. But the model
become worse after that.
I Model the protein using homology modeling and needed it for docking

I am also doing it with different protein molecules but again the same
problem occurs.
I don't know that its normal or there is problem with my parameter or force
field.
I am also mentioning the detail of my energy minimization.

The details are: 
Force Field Used: CHARMM27 all-atom force field
Water Model: TIP3P

em.mdp file is:

; VARIOUS PREPROCESSING OPTIONS = 
title                    = 
cpp                      = /lib/cpp
include                  = 
define                   = -DFLEXIBLE

; RUN CONTROL PARAMETERS = 
integrator               = steep
; start time and timestep in ps = 
tinit                    = 0
dt                       = 0.002
nsteps                   = 15000

; ENERGY MINIMIZATION OPTIONS = 
emtol                    = 10
emstep                   = 0.1
nstcgsteep               = 1000

coulombtype	=pme
nstenergy	=10

Please help me out for this. 


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