[gmx-users] Decane layer

[David van der Spoel]

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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