[gmx-users] Test Particle Insertion of Water
Steven Neumann
s.neumann08 at gmail.com
Wed May 9 15:59:25 CEST 2012
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 <jcb1 at um.es> 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
> --
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