[gmx-users] cpp exitcode 32512; grompp error

Y U Sasidhar sasidhar at chem.iitb.ac.in
Mon Jun 30 14:19:01 CEST 2003


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
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

-- 
 Sasidhar






More information about the gromacs.org_gmx-users mailing list