[gmx-users] RE: em in normal modes analysis

[vincenzo venditti]

Hi all,
I am trying to energy minimize my protein for a NMA. I've compiled GROMACS 
in double precision version and I'm using this .mdp file:
------------------------------------------------------------------------------------------------------------------------------------------
title               = 1P67_R2C_E9C
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  10000
nstlist             =  10
ns_type             =  grid
nstcgsteep           =  100
rlist               =  0.9
coulombtype		=  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing		=  0.12
fourier_nx		=  0
fourier_ny		=  0
fourier_nz		=  0
pme_order		=  6
ewald_rtol		=  1e-5
optimize_fft		=  yes
;
;       Energy minimizing stuff
;
emtol               =  0.001
emstep              =  0.01
--------------------------------------------------------------------------------------------------------------------------------------

Nevertheless in the .log file I find :

Polak-Ribiere Conjugate Gradients converged to machine precision in 187 
steps,
but did not reach the requested Fmax < 0.001.
Potential Energy  = -3.47556312352537e+04
Maximum force     =  8.04322685559554e+00 on atom 250
Norm of force     =  4.12079516782199e-01

What can I do to improve my energy minimization?

Thanks,
Vincenzo

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