[gmx-users] mdp file help

Christopher Stiles CS145331 at albany.edu
Wed Jul 18 16:08:30 CEST 2007

I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble with the mdp
file, basicly what should and should not be in it. I just want it generic to
start and tune it up later. Here is what I have done so far along with links
to copys of the files I have used:




Must have the following files in the working directory to start:


Can find a copy at: http://cs86.com/CNSE/SWNT_6_6_144.pdb



**** must change this files name to ffG43b1.n2t and add the following 2

C       C       1       C                               ; CNT Carbon with
one bond

C       C       2       C       C                       ; CNT double bonded



add the following line to it:

C    C    1   0.14210     478900.



*** you can find copies of both of these files at the following location:



x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

***Note: for some reason it does not generate SWNT_6_6_144.rtp


editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro  -d 0.5


genbox -cp SWNT_6_6_144.gro  -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -maxsol 300


grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -o -maxwarn




#### em3.mdp###  Can find a copy at: http://cs86.com/CNSE/em3.mdp


title                    = SWNT_6_6_144

cpp                      = cpp

include                  = /usr/local/gromacs/share/gromacs/top/

define                   = -DFLEX_SPC

integrator               = md

dt                       = 0.002

nsteps                   = 500000

nstxout                  = 5000

nstvout                  = 5000

nstlog                   = 5000

nstenergy                = 250

nstxtcout                = 250

xtc_grps                 = Protein

energygrps               = Protein  SOL

nstlist                  = 10

ns_type                  = grid

rlist                    = 0.8

coulombtype              = cut-off

rcoulomb                 = 1.4

rvdw                     = 0.8

tcoupl                   = Berendsen

tc-grps                  = Protein      SOL

tau_t                    = 0.1  0.1

ref_t                    = 300  300

Pcoupl                   = Berendsen

tau_p                    = 1.0

compressibility          = 4.5e-5

ref_p                    = 1.0

gen_vel                  = yes

gen_temp                 = 300

gen_seed                 = 173529

constraints              = all-bonds




This is what I get after running grommp:




-bash-3.00$ grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
-o -maxwarn 310

                         :-)  G  R  O  M  A  C  S  (-:





  -[no]renum   bool    yes  Renumber atomtypes and minimize number of



creating statusfile for 1 node...

' for variable integrator, using 'md'

Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'

' 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' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'

' for variable tcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'

' for variable Pcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'

' 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.15#

checking input for internal consistency...

...ling cpp

: command not found

cpp exit code: 32512

 SWNT_6_6_144.top > gromppOpff2m'cs/top -DFLEX_SPC

' command is defined in the .mdp file

processing topology...

processing coordinates...


Program grompp, VERSION 3.3.1

Source code file: futil.c, line: 340


File input/output error:




"This May Come As a Shock" (F. Black)






Any help or advice is greatly appreciated!


~Christopher Stiles 
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
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