Dear GROMACS users,
Thanks for all the replies. They're very helpful. Actually, i have no
expertise in this field around me. Moreover i'm from chemistry, so statistical
and quantum mechanics are no familiar to me. Thats made my progress become
slower (but not impossible right?).
I have done several simualtions using the .mdp file that i modify from the
example included in the online manual. I'm using the OPLS-AA force field with
the reason i'm doing liquid simulations. I have succeeded in doing some
simulations (as a practice), got some problems and i solved it most based on
these helpful mailing-lists. Its just that i wan to make sure what i'm doing is
right until now.
I am doing MD simulation on the mixture of Oleyl oleate (palm oil ester) /
Sorbitan Monolaurate (Surfactant) in water. The composition is based on
experimental results. I packed these molecules using Packmol (excluding
water).I added water molecules using genbox in calculated box size. After
conjugated-gradients and steepest descents energy minimizations, i run MD
simulation.
Here's my .mdp file.. any comments and suggestions are very welcomed and
helpful.
title = MICELLE #7
cpp = cpp
include = -I/usr/local/gromacs/share/gromacs/top
define =
integrator = md
dt = 0.001
nsteps = 5000000
emtol = 50.0
emstep = 0.01
niter = 20
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 50000
nstvout = 50000
nstlog = 5000
nstenergy = 250
nstxtcout = 250
xtc-precision = 1000
xtc_grps = System
energygrps = System
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.8
coulombtype = cut-off
rcoulomb = 1.2
vdw-type = Cut-off
rvdw = 0.8
table-extension = 10.0
pme_order = 4
ewald_rtol = 1e-05
tcoupl = Berendsen
tc-grps = System
tau_t = 0.1
ref_t = 298
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.01325
gen_vel = yes
gen_temp = 298
gen_seed = 173529
constraints = none
Thank You for reading.
-------------------------------------------------------------------------------------------------------------------------------------
M. Alif M. Latif
Chemistry Department, Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang, Selangor,
Malaysia
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