[gmx-users] rlist

[Justin Lemkul]

On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
> 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?

Again, there is no standard value here and it is dictated by the 
functional form being used. You have a custom interaction potential, 
even if you're using normal PME alongside you have user-defined, 
tabulated vdW interactions. Presumably there should be some evaluation 
of what cutoffs are used to satisfy whatever the assumptions are in the 
parametrization of your model, i.e. you need to have some target data of 
a known system that tells you that your physical model (cutoffs and 
functional form) is right, and then you use those same settings in 
whatever systems are of interest.

-Justin

> 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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-- 
==================================================

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

==================================================