Hi everybody, I keep having difficulties when trying to use the double precision version of Gromacs. Typically i get infinte forces at step one of a simulation with double precision while the same system behaves perfectly well with single precision.
Below i give an example of what i see when i try to minimize
a short peptide in vacuum, the input files (pdb and mdp)
are attached.
I wonder if anybody else sees similar problems and has possibly
found a solution.
thanks in advance for any help or suggestions!
Michael
example:
I start with the speptide.pdb file from the gmx tutorial,
and proceed as follows...
(details about hardware etc below)
1) include as first line:
"CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 "
into speptide.pdb.
2) make topology (use GROMOS96 43a1 force field)
echo "0" | pdb2gmx -f speptide.pdb
3) use grompp and mdrun, single precision to minimize the
short peptide in vacuum for 100 steps.
grompp -f em.mdp -c conf.gro -p topol.top -o s.tpr
mdrun -v -s s.tpr
gives:
Step= 0, Dmax= 1.0e-02 nm, Epot= 2.94552e+02 Fmax= 6.05693e+03, atom= 120
Step= 1, Dmax= 1.0e-02 nm, Epot= 5.33718e+01 Fmax= 5.18432e+03, atom= 83
Step= 3, Dmax= 6.0e-03 nm, Epot= -1.56387e+02 Fmax= 2.95143e+03, atom= 120
Step= 5, Dmax= 3.6e-03 nm, Epot= -2.14290e+02 Fmax= 1.68914e+03, atom= 81
Step= 7, Dmax= 2.2e-03 nm, Epot= -2.49216e+02 Fmax= 1.55114e+03, atom= 120
etc...
simulation finishes and gives expected result.
5) use grompp_d and mdrun_d, double precision.
grompp_d -f em.mdp -c conf.gro -p topol.top -o d.tpr
mdrun_d -v -s d.tpr
gives:
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.18566e+03 Fmax= inf, atom= 1
Step= 34, Dmax= 1.2e-12 nm, Epot= -2.18566e+03 Fmax= inf, atom= 1
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 200
... simulation finishes and the coordinates in the confout,gro
are EXACTLY the same as in the input (apart from the fact
that the molecule is shifted by a boxlength, because the first
atom of the input structure is outside the box)
more details:
*) the gmx double precision version was compiled exactly as
suggested in the INSTALL file.
*) my soft/hardware: gmx-3.3.2 on a PC, AMD Turion 64,
linux-2.6.23, gcc-4.2.3
... though i see the same behaviour with the current
(todays) cvs version of gmx on the same hardware,
and with gmx-3.3.1 on a 32-bit PC
*) i see similar problems with other systems, i.e., in many
(but not all) cases single precision works, double gives
problems...
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em.mdp
Description: 462865951-em.mdp
speptide.pdb
Description: 3672131110-speptide.pdb
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