[gmx-users] energy minimization using double precision gromacs failed
sp1020 at gmail.com
Mon Aug 13 15:18:42 CEST 2007
How about trying md with very small step size such as
dt = 0.0001
Once I had similar problem like you and it is solved by performing
additional energy minimization step with very small step size.
I can't guarentee this method, but I think it might be OK.
On 8/13/07, Q733 <sansanqin00 at mails.tsinghua.edu.cn> wrote:
> 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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'God used beautiful mathematics in creating the world.'
'But he created too many object.'
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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