[gmx-users] rlist
Faezeh Pousaneh
fpoosaneh at gmail.com
Sun Jan 14 17:40:15 CET 2018
Thanks a lot,
Best regards
On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin, now I understood. However, I do not have any target data
>> for my system. What do you suggest? the longer rcoulomb is safer, right?
>>
>
> Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
> any specific value. It depends on your model. You have to demonstrate to a
> skeptical audience that your methods are sound. That requires describing a
> known system and its structure, energetics, and dynamics. Then you can move
> to predicting unknowns. Without that, there's no control to determine if
> your work is meaningful or a random number generator.
>
>
> -Justin
>
>
>> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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