[gmx-users] rlist

[Faezeh Pousaneh]

Thanks Justin. But I only define vdW potential form, coulomb potential form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are

  rlist                 = 0.9  (in nm)
  rcoulomb        = 0.9  (in nm)

fine while I am using PME?

Best regards


On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I have a system of charged hard spheres (user-potential), where the vdW
>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose
>> rlist
>> and rcoulomb correctly? (see below please)
>>
>
> I'm not sure if anyone can tell you that. You're using custom potentials,
> so setting cutoffs is part of the parametrization of that potential itself.
>
> -Justin
>
>
> integrator                = md
>>   dt                        = 0.001
>>   nsteps                    = 30000000
>>   nstxout                   = 100000           ; save coordinates every 0
>> ps
>>   nstvout                   = 100000           ; save velocities every 0
>> ps
>>   nstlog                    = 100000           ; update log file every
>>   nstenergy                 = 100000        ; save energies every
>>   nstxtcout                 = 100000       ; Output frequency for xtc file
>>   xtc-precision             = 100000       ; precision for xtc file
>>   ns_type                   = grid        ; search neighboring grid cells
>>   nstlist                   = 10           ;  fs
>>   pbc                       = xyz         ; 3-D PBC
>>   rlist                          = 0.9         ; short-range neighbor-list
>> cutoff (in nm)
>>   rcoulomb                  = 0.9         ; short-range electrostatic
>> cutoff
>> (in nm)
>>   rvdw                      = 0.3479      ; short-range van der Waals
>> cutoff
>> (in nm)
>>   coulombtype               = PME-user         ; Particle Mesh Ewald for
>> long-range electrostatics
>>   pme_order                 = 4           ; cubic interpolation
>>   fourierspacing            = 0.16        ; grid spacing for FFT
>>   vdw-type                  = user
>>   Tcoupl                    = berendsen   ; modified Berendsen thermostat
>>   tc-grps                   = co2   rest           ; two coupling groups -
>> more accurate
>>   tau_t                     =  0.1   0.1 ; time constant, in ps
>>   ref_t                     =  179.8  179.8 ; reference temperature, one
>> for
>> each group, in K
>>   ;tc-grps                  = system
>> cutoff-scheme              =group
>>   energygrps                = co2 rest
>>   Pcoupl                    =  berendsen ;Parrinello-Rahman
>>   Pcoupltype                = Isotropic
>>   tau_p                     = 1.0
>>   compressibility           = 6.2e-5
>>   ref_p                     = 5500.0
>>   gen_vel                   = yes
>>   gen_temp                  = 179.8
>>   gen_seed                  = 712349
>>   DispCorr                  =no;  EnerPres    ; account for cut-off vdW
>> scheme
>>   constraints               = all-bonds   ; all bonds constrained (fixed
>> length)
>>   continuation              = no         ; Restarting after NPT
>>   constraint-algorithm      =  lincs       ; holonomic constraints
>>   lincs_iter                = 1           ; accuracy of LINCS
>>   lincs_order               = 4           ; also related to accuracy
>> Best regards
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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