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

[Alan Dodd]

There's probably a problem either with your structure or your topology.  Spend some time looking at what you've done.  I'd start by investigating atom 483.  It should be pretty obvious what's wrong, with a force like that.

----- Original Message ----
From: Q733 <sansanqin00 at mails.tsinghua.edu.cn>
To: gmx-users at gromacs.org
Sent: Monday, August 13, 2007 10:08:34 AM
Subject: [gmx-users] energy minimization using double precision gromacs failed


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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