[gmx-users] Decane layer

Kai Zhuang kai.zhuang at gmail.com
Fri Aug 5 19:02:20 CEST 2005


> if all else fails you can make the box bigger using editconf and run
> with pressure coupling to have it contract again.

can you elaborate on this method?
so you make a box that's much bigger than the current solvent+solution
box, and let the molecules drift around to fill the bigger box, and
then apply pressure to compress the solven + solute back to its
original size? how does this fix bad contacts?


On 8/5/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> On Fri, 2005-08-05 at 15:40 +0100, M.Naser wrote:
> > Thnaks david.
> >
> > Can you give me some idea of how long it suppose to take?
> unless the conformation is really bad a few hundred steps should
> suffice. then you should run with pressure coupling.
> 
> if all else fails you can make the box bigger using editconf and run
> with pressure coupling to have it contract again.
> >
> >
> >
> >
> >
> > > On Fri, 2005-08-05 at 15:19 +0100, M.Naser wrote:
> > >> Hi All,
> > >>
> > >> I have a decane box with 730 kg/m^3 and trying to run trial simulation
> > >> but
> > >> crashing on me. It might be due to the bad contact. Is there any way I
> > >> can
> > >> avoid that?
> > >
> > > long energy minimization
> > >
> > >>
> > >> My mdp file as follows:
> > >>
> > >> title                  =  Decane
> > >> cpp                 =  /lib/cpp
> > >> ;define              =  -DPOSRES ;  -DFLEX_SPC  -DFLEXIBLE
> > >> ;include             =  -I/home/bio/mn2/tutor/project1/
> > >>
> > >> integrator          = md
> > >> dt                  = 0.001
> > >> nsteps              = 1000000
> > >> tint                   = 0
> > >> init_step           = 0
> > >> comm_mode           = linear
> > >> nstcomm             = 1
> > >>
> > >>
> > >>
> > >>
> > >> nstlist             = 10
> > >> ns_type        = grid
> > >> pbc                 = xyz
> > >> rlist                  = 0.9
> > >>
> > >>
> > >>
> > >>
> > >> coulombtype            = PME
> > >> rcoulomb-switch     = 0
> > >> rcoulomb            = 0.9
> > >> vdwtype                = switch
> > >> rvdw-switch            = 0.8
> > >> rvdw                = 0.9
> > >> fourierspacing     = 0.1
> > >> pme_order          = 4
> > >> ewald_rtol          =1e-5
> > >> ewald_geometry      =3dc
> > >> surface_epsilon     =0
> > >> optimize_fft        =yes
> > >> DispCorr            = no
> > >> table-extension     = 1
> > >>
> > >> Tcoupl              =  Berendsen
> > >> tc_grps                = system
> > >> tau_t               =  0.1
> > >> ref_t                  =  300
> > >>
> > >> Pcoupl              = no
> > >>
> > >> constraints               = all-bonds
> > >> constraint_algorithm      = shake ;lincs
> > >> unconstrained_start       = no
> > >> shake_tol                 = 0.0001
> > >>
> > >>
> > >> nstxout            = 1000
> > >> nstvout            = 1000
> > >> nstfout            = 0
> > >> nstlog            =  1000
> > >> nstenergy         =  1000
> > >> nstxtcout         =  1000
> > >> xtc_precision     = 1000
> > >>
> > >> Thanks in advance,
> > >>
> > >> Abu
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> __________________________________________________________________
> > >>
> > >> DISCLAIMER:
> > >>
> > >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> > >> __________________________________________________________________
> > >> _______________________________________________
> > >> gmx-users mailing list
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> > >> http://www.gromacs.org/mailman/listinfo/gmx-users
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> > > --
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > > phone:  46 18 471 4205          fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > __________________________________________________________________
> >
> > DISCLAIMER:
> >
> > This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> > __________________________________________________________________
> > _______________________________________________
> > gmx-users mailing list
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
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-- 
---------------------------------------------------------------------------------------------------------------------------------
MD simulations reminds me of my first year CompSci project where a
"hobbit" object has to randomly avoids a bunch of "orc" objects.  yay
for LOTR.
--------------------------------------------------------------------------------------
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
6478314789



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