[gmx-users] MD run error

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Fri Jan 6 19:39:26 CET 2006

You have used one undefined swich in mdp file. I think it is "warning"

Yang Ye

Mahalakshmi S <mlakshmis at iitm.ac.in> wrote: Dear All,

I am a newbie to gromacs.
I am trying to do a MD simulation for 2ns at constant temperature of 298K 
and a constant pressure of 1atm. Temperature and pressure were 
regulated by weak coupling to an external bath and 
electrostatics was dealt by using a 8angstrom Coulombic cut-off. I 
fully solvated the structure with SPC water in a cubic box with a 20 
angstrom edge length. I did energy minimization for the structure using 
steepest descents for 1000 steps and a position restrained MD run. I want 
the system to eveolve according to Newton's equation of motion, with 
equations being integrated every 2fs. I am trying to do a full MD and I am 
getting error. I am attaching the full.mdp file. Below you would find the 
errors which I got. Please let me know whats wrong wit my full.mdp or how 
could I correct this error.

I executed this command :

grompp -v -f full.mdp -o full.tpr -c after_pr.grp -p ubq.top.

It gives me the following error :
  reating statusfile for 1 node...
  Sorry couldn't backup mdout.mdp to ./#mdout.mdp.2#
  WARNING 1 [file full.mdp, line unknown]:
   Unknown left-hand warnings in parameter file

checking input for internal consistency...
calling /usr/bin/cpp...
sh: gromppmMKf08: No such file or directory
cpp exit code: 256
Tried to execute: '/usr/bin/cpp  -I/usr/local/share/gromacs/top  ubq.top >
The '/usr/bin/cpp' command is defined in the .mdp file
processing topology...
Cleaning up temporary file gromppmMKf08
Fatal error: Could not open gromppmMKf08

title= ubq
warnings = 10
cpp = /usr/bin/cpp
integrator = md
dt = 0.002
nsteps = 1000000
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
; Neighbour Searching
ns_type = grid
; Electrostatics and VdW
rlist = 0.9
coulombtype = PME
rcoulomb = 0.8
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1 
tc-grps = protein sol
ref_t = 298  298
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; Generate velocities is on at 300 K.
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
constraints = all-bonds
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