[gmx-users] question about Polak Ribiere conjugate gradient
David
spoel at xray.bmc.uu.se
Mon May 3 14:49:04 CEST 2004
On Mon, 2004-05-03 at 14:08, Hua Wong wrote:
> I am doing a minimization using the brand new GROMACS 3.2. It works fine on a system that previously lead to error with GROMACS 3.1.
>
> I am working on a protein minimised under NAMD and wanted to minimise it further using GROMACS to correct some omega torsion problems. All seems to be fine, only I obtain a warning :
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1e-06
>
> I am using CG with GROMACS compiled in double precision.
>
try using
integrator = l-bfgs
> Here is the .mdp file I use.
> ##################################
> title = GMXminiomega
> cpp = /lib/cpp
> include = -I../top
> define = -DFLEXIBLE
> integrator = cg
> emtol = 0.000001
> emstep = 0.01
> nstcgsteep = 100
> nsteps = 3000
> nstxout = 50
> xtc_grps = Protein
> energygrps = Protein
> nstlist = 5
> ns_type = grid
> rlist = 1.
> vdwtype = cut-off
> coulombtype = cut-off
> rcoulomb = 1.
> rvdw = 1.
>
> Is there anything I've forgotten ?
>
> Thanks
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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