[gmx-users] Some poblems~

F JH juhow1011 at hotmail.com
Thu Feb 19 17:08:01 CET 2004

Dear GMX users:

It seems that double precision must be activated by "--disable-float" but I 
found an  interesting phenomenon on my Linux platform
1.use "./configure --enable-mpi --disable-float" and compile GROMACS.I 
think I've compiled GROMACS with MPI and double precison.But I found the 
message when I used mdrun

"Reading file topol.tpr, VERSION 3.1.4 (single precision)"
  Reading file topol.tpr, VERSION 3.1.4 (single precision)
It seems double precision not work
2.use "./configure --disable-float" and "./configure --enable-mpi" 
individually and found the following messges
* You are compiling a double precision version of the package -
    program names will be suffixed with _d to avoid overwriting single
    precision files. You can override it with --program-suffix
* Seems you are compiling with MPI support. You can install the MPI-
   enabled programs with suffixed names to have both MPI and non-MPI
   versions. This is useful e.g. on supercomputers where you usually
   cannot run MPI-linked programs on the login node.
   Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
   You only need MPI for mdrun, so if you already have non-MPI stuff
   installed you can issue make mdrun; make install-mdrun.
Does it means I 've only compiled MPI,not double precison?

3.When I run a minmization job with "single precision"(maybe),I found the 
following messages

Negative w:  -6.111514486374e+13
z=  -3.430048800000e+07
gpa=   2.322916848568e+07, gpb=   5.327950593513e+07
a=   0.000000000000e+00, b=   7.583112298282e-07
EpotA=  -5.510806152344e+03, EpotB=  -5.482796875000e+03
Negative number for sqrt encountered (-61115144863744.000000)
Terminating minimization
writing lowest energy coordinates.
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up confout.gro to ./#confout.gro.1#
Conjugate Gradients did not converge in 403 steps
Potential Energy  = -5.51081e+03
Maximum force:  1.73107e+03
I searched the forum and found maybe it's the result when using single 
precision.Is my supposiiton correct?

4.Finally,everytime I used grompp.I always found the waring "protein has 
non-zero total charge"
Is it a risk for my job?or how could I improve it?

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