[gmx-users] mdp file help
james zhang
james.zhangj at gmail.com
Wed Jul 18 16:44:58 CEST 2007
You can get a typical mdp file from some tutorials.
By the way, I think the topology is wrong.
Thanks.
On 7/18/07, Christopher Stiles <CS145331 at albany.edu> wrote:
>
> 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:
>
> SWNT_6_6_144.pdb
>
> Can find a copy at: http://cs86.com/CNSE/SWNT_6_6_144.pdb
>
>
>
> ffgmx.n2t
>
> **** must change this files name to ffG43b1.n2t and add the following 2
> lines:
>
> C C 1 C ; CNT Carbon with
> one bond
>
> C C 2 C C ; CNT double
> bonded Carbon
>
>
>
> ffgmxbon.itp
>
> 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:
>
> /usr/local/gromacs/share/gromacs/top/
>
>
>
> 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
> 310
>
>
>
>
> ***********************************************************************************************
>
>
>
> #### 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
>
> atomtypes
>
>
>
> 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'
> 'Andersen-interval'
>
> ' 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:
>
> conf.gro
>
> -------------------------------------------------------
>
>
>
> "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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--
Sincerely yours,
James Jianzhang
Department of Mechanical and Chemical Engineering
North Carolina Agricultural and Technical State University
1601 East Market Street
Greensboro, NC 27411
jzhang at ncat.edu or james.zhangj at gmail.com
http://www.ncat.edu/~jzhang
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