[gmx-users] rlist
Justin Lemkul
jalemkul at vt.edu
Sun Jan 14 17:32:34 CET 2018
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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>> * Please search the archive at http://www.gromacs.org/Support
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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
==================================================
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