[gmx-users] Test Particle Insertion of Water

[Steven Neumann]

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120509/ed61f1a2/attachment.html>