[gmx-users] energy minimization using double precision gromacs failed

Q733 sansanqin00 at mails.tsinghua.edu.cn
Mon Aug 13 11:08:34 CEST 2007


Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of
32 lipids(16 up and 16 down) with two water layers(428 up and 428 down).
my em.mdp is like this:

title                    = 
cpp                      = /lib/cpp 
include                  = 
define                  = -DFLEXIBLE
constraints 		 = none ;h-bonds
lincs_iter		 = 4

; RUN CONTROL PARAMETERS = 
integrator               = l-bfgs

tinit                    = 0
dt                       = 0.2	; ps
nsteps                   = 6000

nstxtcout				= 100     ; pos to xtc file

nstlist					= 5
ns_type					= grid
rlist						= 0.7
coulombtype				= PME
rcoulomb					= 0.7
vdw-type					= Cut-off
rvdw						= 0.7
fourierspacing			= 0.095	; default to 0.12
fourier_nx				= 0
fourier_ny				= 0
fourier_nz				= 0
pme_order				= 4
ewald_rtol				= 1e-5
optimize_fft			= yes

; ENERGY MINIMIZATION OPTIONS = 
emtol						= 0.00001	; default to 100
emstep					= 0.5		; default to 0.01
nstcgsteep				= 1000

The em is done using double-precision gromacs program,and the out put is
like this:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1e-05

writing lowest energy coordinates.

Low-Memory BFGS Minimizer converged to machine precision in 7 steps,
but did not reach the requested Fmax < 1e-05.
Potential Energy  =  1.25811048952284e+15
Maximum force     =  5.23956606456297e+17 on atom 483
Norm of force     =  6.77707038974525e+15

How can I prevent it from converging to machine precision? Is there any
method to change the standard of machine precision?
Any suggestion will be appreciated , thanks a lot.




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