[gmx-users] rlist
Faezeh Pousaneh
fpoosaneh at gmail.com
Sun Jan 14 17:30:19 CET 2018
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?
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
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list