[gmx-users] mdp file to calculate local pressure
Justin A. Lemkul
jalemkul at vt.edu
Fri May 22 13:23:21 CEST 2009
anirban polley wrote:
> Dear Justin,
> I am using gromacs-localp of version 4.0.2. for the calculation of
> local pressure. But I could not understand what I should put in the mdp
> file. Because when I tried by the following below mdp file, it does not
> even create tpr file. I have tried by different options as for example
> by using Wall but failed to get local pressure profile. I thought that I
> have write some thing so that it can be ok for giving local pressure.
> Could you please correct my mdp file and write what extra term I should
> write in my mdp file to get local pressure.
> Thank you very much for your kind help.
Where did you get gromacs-localp version 4.0.2? The software by that name in
the Users Contributions is much older. If you have made modifications to the
code yourself, you may have broken something.
As I understand it, the .mdp file is probably going to be the same as any other
run, you'll just get additional output for local pressure. That information is
likely in whatever README or help files that come with the localp code.
Also, if grompp is failing to produce your .tpr, it is better to post the error
message you got instead of saying "it does not even create tpr file." For
diagnostic purposes, a real error message is infinitely more useful.
> title = lipid bilayer in water
> cpp = /lib/cpp
> integrator = sd ; stochastic dynamics -> Langevin!
> ld_seed = -1 ; random seed for sd
> dt = 0.002 ; ps !
> nsteps = 250000 ; total 500 ps
> nstcomm = 1 ; freq. for cm-motion removal
> tinit = 0 ; starting time (ps)
> constraints = all-bonds ; constraint for all bond lengths
> constraint_algorithm = lincs ; default
> lincs_order = 4 ; default
> nstxout = 5000 ; T(x_out) 10 ps
> nstvout = 5000 ; T(v_out) 10 ps
> nstfout = 0 ; T(f_out)
> nstlog = 250 ; energies to log (0.5 ps)
> nstenergy = 250 ; energies to energy file
> ns_type = grid ; nl type
> nstlist = 10 ; Freq. to update neighbour list
> rlist = 1.0 ; nm (cutoff for short-range nl)
> coulombtype = Reaction-Field ; Coulomb interactions
> rcoulomb = 2.0 ; nm (Coulomb cut-off!!)
> epsilon_r = 80.0 ; dielectric constant for
> reaction field
> vdwtype = Cut-off ; Wan der Waals interactions
> rvdw = 1.0 ; nm (LJ cut-off)
> optimize_fft = yes
> ; Temperature coupling
> Tcoupl = no ; no effect when integrator = sd
> tc-grps = POPC SM CHOL SOL
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 296 296 296 296
> ; Pressure coupling
> ;Pcoupl = no
> Pcoupl = berendsen
> Pcoupltype = semiisotropic
> tau_p = 1.0 1.0 ; ps
> compressibility = 4.5e-5 4.5e-5 ; 1/bar (water: 1 atm, 300 K)
> ref_p = 1.0 1.0 ; bar
> ; Generate velocites in the beginning
> gen_vel = yes
> gen_temp = 296.0
> gen_seed = 173529
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users