[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
> > >> __________________________________________________________________
> > >> _______________________________________________
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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
> > __________________________________________________________________
> > _______________________________________________
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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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