[gmx-users] Decane layer
David
spoel at xray.bmc.uu.se
Fri Aug 5 20:16:50 CEST 2005
On Fri, 2005-08-05 at 13:02 -0400, Kai Zhuang wrote:
> > 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?
yes. since the box is big in the beginning there are no 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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>
>
--
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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