On 2012-05-04 00:37, Dallas Warren wrote:
Did you plot the box volume, box dimensions or density with simulation time?
Over those 500,000 steps it should be shrinking.
It would also be a good idea if you made a box size and number of molecules
that is at least close to the density of octanol. From the image you included,
the box appears to be at least 3 times too large for the number of molecules
you have inserted.
Or you go to the gromacs molecule & liquid database:
http://virtualchemistry.org/molecules/111-87-5/index.php
Octanol is a bitch, slow to converge anything because it is big.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
[email protected]
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: [email protected] [mailto:gmx-users-
[email protected]] On Behalf Of Ondrej Kroutil
Sent: Thursday, 3 May 2012 8:23 PM
To: [email protected]
Subject: [gmx-users] Proper 1-octanol box preparation
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--
Ondřej Kroutil
,, Faculty of Health and Social Studies
----"))' University of South Bohemia
OOO Jirovcova 24, Ceske Budejovice
OOO The Czech Republic
| OO E-mail: [email protected]
------ O Mobile: +420 736 537 190
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