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.
-Justin
Anirban
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
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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