[gmx-users] energy minimization of DNA in water

[Kristina Woods]

Hi there,

I have been trying to minimze a fragment of DNA in water for a normal
mode analysis...but without much luck.

I am using a .mdp file for the energy minimization that looks like this:
-----------------------------------------------------------------------
cpp                 = /usr/bin/cpp
include             =  -I/usr0/user/kwoods/gromacs/DNA_normal/53a6
-I/usr0/user/kwoods/gromacs/gromacs-3.2.1/share/top
define              =  -DFLEXIBLE
integrator          =  cg
constraints         =  none
nsteps              =  500000
;
;       Energy minimizing stuff
;
emtol               =  0.00001
emstep              =  0.00001
nstcgsteep          =  100        
coulombtype         = PME
rvdw                = 1.4
rlist               = 1.4 
rcoulomb            = 1.4 
fourierspacing      = 0.12 
pme_order           = 4
ewald_rtol          = 1e-5
vdwtype             = shift
ns_type             = grid
dispcorr            = enerpres
nstxout             = 50
xtc_grps            = system
energygrps          = system
nstlist             = 10
-----------------------------------------------------------------------

But here are the lowest energy coordinates that I can achieve:

writing lowest energy coordinates.

Polak-Ribiere Conjugate Gradients converged to machine precision in 147 steps,
but did not reach the requested Fmax < 1e-05.
Potential Energy  = -2.41706441033253e+04
Maximum force     =  1.74065672764869e+00 on atom 875
Norm of force     =  1.92397357924797e-01

-------------------------------------
I was wondering if anyone has any suggestions on how to achieve better
energy minimization results?  Or identify something that is obviously
wrong?

Thank you,

Kristina :)