[gmx-users] Decane layer

[M.Naser]

Thnaks david.

Can you give me some idea of how long it suppose to take?





> 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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> --
> 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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