[gmx-users] Proper 1-octanol box preparation

[Dallas Warren]

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.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Ondrej Kroutil
> Sent: Thursday, 3 May 2012 8:23 PM
> To: gmx-users at gromacs.org
> 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:  okroutil at gmail.com
> >------    O         Mobile:  +420 736 537 190
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