[gmx-users] Proper 1-octanol box preparation

[David van der Spoel]

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
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se