grompp -f tpi.mdp -c tpi.pdb -p topol.top -o tpi.tpr where tpi.pdb is a file with extra water molecule as well as topol.top. Then:
mdrun –s tpi.tpr -rerun md.trr -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg On Wed, May 9, 2012 at 2:56 PM, Javier Cerezo <[email protected]> wrote: > What's your command line? > > El 09/05/12 15:49, Steven Neumann escribió: > > title = Test Particle Insertion >> ; Run parameters >> integrator = tpi >> nsteps = 50000000 ; 100 ns >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 0 ; suppress .trr output ; output coordinates >> every 25 ps >> nstvout = 25000 ; velocities to output every 25000 steps >> nstenergy = 1000 ; save energies every 2 ps >> nstlog = 1000 ; update log file every 2 ps >> nstxtcout = 100000 ; suppress (tlumic) xtc trajectory >> energygrps = System >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> vdwtype = Switch >> rvdw-switch = 1.0 >> rlist = 1.4 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.2 ; short-range van der Waals cutoff (in nm) >> ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted >> potential rcoulomb >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.12 ; grid spacing for FFT >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen >> thermostat >> tc_grps = System ; two coupling groups - more accurate >> tau_t = 0.1 ; time constant, in ps >> ref_t = 318 ; reference temperature, one >> for each group, in K >> ; Pressure coupling is on >> pcoupl = Parrinello-Rahman ; pressure coupling is on for >> NPT >> pcoupltype = isotropic ; uniform scaling of box >> vectors >> tau_p = 2.0 ; time constant, in ps >> ref_p = 1.0 ; reference pressure, in bar >> compressibility = 4.5e-5 ; isothermal compressibility >> of water, bar^-1 >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; Dispersion correction >> DispCorr = EnerPres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = yes ; assign velocities from Maxwell distribution >> gen_temp = 318 ; temperature for Maxwell distribution >> gen_seed = -1 ; generate a random seed >> > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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