[gmx-users] cpp exitcode 32512; grompp error

[David van der Spoel]

On Mon, 2003-06-30 at 14:18, Y U Sasidhar wrote:
> We have encountered the following grompp error prior to energy 
> minimization of a peptide in spc water using steep:
> On archives also a few people reported this error, but no clear answer 
> except that mdp file may  be badly created.
> we tried to play with mdp file by adding , deleting lines etc but  to no 
> avail.
> What kind of error (in mdp file ? )  can cause this error ?
> =============error message======================
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> ...ling /lib/cpp
> : No such file or directory
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

replace the line cpp = /lib/cpp by something else appropriate for your
system. If necessary install a compiler.

> cpp exit code: 32512
>  betahair.top > grompp6gfnPT'top -DFLEX_SPC
> ' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (solvation.gro, 6191)
>              does not match topology (betahair.top, 0)
> ===================================
> our_comment:( total number of atoms do match by visual inspection )
> ===========================
> mdp file for em
> ==============================
> cpp = /lib/cpp
> define = -DFLEX_SPC
> integrator = steep
> nsteps = 300
> emtol = 2000
> emstep = 0.01
> nstxout = 25
> nstvout = 25
> nstlist = 10
> nstenergy = 25
> nstcomm = 1
> ns_type = grid
> rlist = 1.5
> rcoulomb = 1.5
> rvdw = 1.5
> rcoulomb_switch = 1.0
> rvdw_switch = 0.9
> coulombtype = shift
> vdwtype = shift
> Tcoupl = berendsen
> tc_grps    = Protein SOL
> tau_t    =   0.1     0.1
> ref_t =     300     300
> energygrps = Protein SOL
> Pcoupl = no
> gen_vel = no
> gen_temp = 300
> gen_seed = 173529
> constraints = none
> constraint_algorithm = lincs
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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