[gmx-users] Decane layer

[David van der Spoel]

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
> 
> 
> 
> 
> 
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> 
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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
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