[gmx-users] question about Polak Ribiere conjugate gradient
lindahl at csb.stanford.edu
Mon May 3 15:06:02 CEST 2004
1e-6 kJ/mol is a very tough energy tolerance for a big system :-)
In general, if you apprioximate the energy surface close to the minimum
with harmonic potentials, you cannot do better than sqrt(machine
precision) in both the coordinate and value.
Considering a protein consists of thousands of degrees of freedom
you'll have some rounding errors too, so I would be very surprised if
you could get to 1e-6.
And, remember, all you can hope for is a *local* minimum. With that in
mind there is rarely any reason to go lower than 0.1 kJ/mol...
On May 3, 2004, at 4:49 PM, David wrote:
> 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 ?
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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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