[gmx-users] Trouble editing mdp file

[p.keymer at student.qut.edu.au]

Hi all

I am a new gromacs user and I atempting to make changes to 
the standar mdp file. 

This is the file i am using:

""
title               =  fws 
cpp                 =  /lib/cpp 
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  50000	; total 100 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  0
nstfout             =  0
nstlist             =  10 
ns_type             =  grid
rlist               =  0.9
coulombtype		=  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing		=  0.12
fourier_nx		=  0
fourier_ny		=  0
fourier_nz		=  0
pme_order		=  6
ewald_rtol		=  1e-5
optimize_fft		=  yes
; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.1	0.1
tc_grps		    =  protein	sol
ref_t               =  300	300
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
""


all I doo is change the nsteps and save it then attempt to 
run grompp.  when I do so the following appears:


""
creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-
Field' 'Generalized-Reaction-
Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes'
' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-
Rahman' 'Isotropic'
' for variable Pcoupltype, using 'Isotropic'
Next time use one 
of: 'Isotropic' 'Semiisotropic' 'Anisotropic' 'Surface-
Tension'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-
angles' 'all-angles'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
Warning: as of GMX v 2.0 unit of compressibility is truly 
1/bar
checking input for internal consistency...
...ling /lib/cpp 
cpp: error 0: No source file 
cpp exit code: 2048
  -I/pkg/gromacs/share/top  pep.top > grompp028037'
' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file 
(after_pr.gro, 2647)
             does not match topology (pep.top, 0)
""

Please can someone help

Thank you in advance

Philip Keymer