[gmx-users] Proper 1-octanol box preparation
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 4 09:40:28 CEST 2012
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:
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
>> 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
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