Hi,
relating to the picture see:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
It's just a matter of periodic boundary conditions, you don't have two,
but just one cluster of octanol.
What i don't understand is, that your box doesn't collapse (becoming
smaller) if you perfom the NPT simulation. Only thing is that i would
search the value of compressibility of octanol, but this couldn't be the
origin of the problem.
Greetings
Thomas
Am 03.05.2012 12:23, schrieb gmx-users-requ...@gromacs.org:
Hi GMX users!
I prepared a box of 125 1-octanol molecules using genconf -f
octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate
this system in NPT ensemble to get proper density and nice cube box,
similar to octanol configuration that one can download from
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies.
But I always got something completely different. Some cluster of the
molecules at the bottom of the simulation box, far away from dense
cube configuration. You can see picture here:
https://picasaweb.google.com/okroutil/Science#5738216101659210130. I
tried different thermo- and barostats, different coupling times,
compressibility, first NVT then NPT equil., but with no success. I
also tried more "chaotic" initial configuration generated with genbox
-ci ...gro - nmol 125 -box 5 5 5, no success.
So my question is: is there some simulation protocol or some setting
(higher pressure at the beginning of equilibration?), any trick
suitable for this type of solvent? Till now I worked only with water
and surfaces, so this is new area for me...
Thank you very much for any answer and have a nice day!
Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian
University, Czech Republic)
P.S.: I used gaff ff and topologies downloaded from
http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT
eq. input:
integrator = md
dt = 0.002
nsteps = 500000
comm_mode = linear
nstcomm = 1000
nstxout = 0
nstxtcout = 100
nstvout = 0
nstfout = 0
nstlog = 500
nstlist = 10
ns_type = grid
rlist = 1.4
coulombtype = PME
rcoulomb = 1.4
rvdw = 1.4
constraints = none
constraint_algorithm = lincs
;shake_tol = 0.00001
lincs_iter = 1
fourierspacing = 0.1
pme_order = 4
ewald_rtol = 1e-5
ewald_geometry = 3d
optimize_fft = yes
; Nose-Hoover temperature coupling
Tcoupl = berendsen
tau_t = 1
tc_grps = system
ref_t = 298.
; No Pressure
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.6e-5
ref_p = 1.0
; OTHER
periodic_molecules = no
pbc = xyz
gen_vel = yes
gen_temp = 298.15
gen_seed = -1--
Ond??ej Kroutil
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