On 1/27/13 11:53 PM, Ewaru wrote:
Dear Gromacs experts,
I am running gromacs for the first time, and this is my em.mdp file.
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.01 ; ps !
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = EnerPres
nsteps = 10000
nstenergy = 1000
nstxtcout = 1000
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
Unfortunately, when running mdrun, I obtained this "Steepest Descents
converged to machine precision in 7559 steps, but did not reach the
requested Fmax < 100."
Please, can somebody tell me what do I need to change in order for it to run
until the requested steps? Also, the RMSD graph obtained does not begins
from zero (how can I make it to?) and it does not converge.
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
Regarding the RMSD, it probably won't converge during EM since the structure
changes at every step. Without seeing your actual command and the snippet of
the .xvg file showing the starting value, it's impossible to say why it doesn't
start at zero. If it is a very small value (i.e. 1e-4 or less) and not exactly
zero, you can consider that to be effectively zero. Just one of the quirks of
floating-point math.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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