[gmx-users] Decane layer

[David]

On Fri, 2005-08-05 at 16:03 +0100, M.Naser wrote:
> Thanks again david.
> 
> Is there any way I can insert protein in a water box instead of other way
> around. I tired with genbox with -ci  and did not work with me.
genbox does that (-cp -cs). It makes a big water box, puts the protein
in the center and cuts out overlapping water molecules.
> 
> With regards,
> 
> Abu
> 
> > 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:
> >> >>
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> >> >> __________________________________________________________________
> >> >> _______________________________________________
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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
> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >
> >> >
> >> > _______________________________________________
> >> > gmx-users mailing list
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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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> 
> 
> 
> __________________________________________________________________
> 
> 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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