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
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
