anirban polley wrote:
Dear Sir,
I want to calculate local pressure of the membrane
(pressure variation with z -axis). I am using gromacs-localp packages.
As I see that all types of errors coming from saying specifically the
option of WALL in .mdp file.
Actually I did not understand clearly what to do in the following options.
The simple answer to me is - why are you using walls? The gromacs-localp
package is based on version 3.0.2, and IIRC walls were introduced much later in
development, probably version 4.0. At least, there is no mention of walls in
any documentation prior to the 4.0 manual.
-Justin
WALLS
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald
nwall = 2
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
Could you please write clearly what to write on above options ??
I am writing here the mdp file what I am using in gromacs-localp package
to calculate local pressure.
integrator = sd ; stochastic dynamics -> Langevin!
ld_seed = -1 ; random seed for sd
dt = 0.002 ; ps !
nsteps = 50000 ; total 500/5=100 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 = 1000 ; T(x_out) 10 ps
nstvout = 1000 ; 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)
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xy
coulombtype = PME ;Reaction-Field ; Coulomb
interactions
rcoulomb = 1.0 ;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
;WALLS
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald
nwall = 2
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
Thanks a lot in advance.
Regards,
Anirban
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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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