[gmx-users] Re: Proper 1-octanol box preparation

[Thomas Schlesier]

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-request at 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