[gmx-users] Some poblems~

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 19 19:14:01 CET 2004

On Fri, 20 Feb 2004, F JH wrote:

>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
you are mixing up versions. you have to doe
./configue --disable float
make clean
make install

>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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David van der Spoel, PhD, Assist. 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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