[gmx-users] Energy Minimization of DNA

[David Crosby]

Hello all, how are you doing today?

I've been trying to get a stable DNA MD simulation to work for me, but I
think my problem lies in an insufficiently energy minimized system prior to
running the pr step.  I'm using the ffamber99 force field and I've
successfully simulated many ns of MD using the sample Dickerson dodecamer
pdb file supplied on the gromacs web site.  However, when I build my own
21mer using NAB (http://casegroup.rutgers.edu/nab.html), I always get LINCS
warnings during the first thousand steps of pr...  Here are my settings for
em:

define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.001 ; ps !
nsteps = 4000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.08
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 8
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 10000.0
emstep = 0.01

here's a sample of the em output: (27 steps sounds awfully short...)

Steepest Descents converged to Fmax < 10000 in 27 steps 
Potential Energy  = -3.4305819e+05
Maximum force     =  5.8583452e+03 on atom 495
Norm of force     =  3.0654459e+02
And here are my settings for pr:

define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 20000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.08
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 8
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 310 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529

and here's the output from the failed pr after about 500 steps:

-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
you
r mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
-------------------------------------------------------

Thanks again for all your help! You folks are lifesavers!  All suggestions
are welcome!

Dave Crosby
UC Irvine, dept of pathology and laboratory medicine