[gmx-users] The sum of the two largest charge group radii (X) is larger than rlist
fpoosaneh at gmail.com
Sun Dec 17 20:29:34 CET 2017
One component I mean system of only one type atom, each atom has two
charged virtual sites. So I can not see from VMD any breaking.
On Dec 17, 2017 8:10 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:
> Dear Justin,
> How can I check that ''input configuration is "broken" across PBC'' ?
> From vmd it is hard to say, since I only have one component system.
What is that one component? If a group of atoms is supposed to be in a
charge group, and it is split across the box, then you need to correct it
with trjconv or (if you are absolutely sure this isn't a problem) override
with grompp -maxwarn (dangerous and generally not wise).
> Best regards
> On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> The sum of the two largest charge group radii (7.984601) is larger than
>> rlist (0.347900).
>> the configuration looks fine across pbc. Everything looks normal.
>> Following is my md. I have user-specified potential so I need to have
>> cut-off values as given below.
>> integrator = md
>> dt = 0.001
>> nsteps = 3000000
>> nstxout = 100000 ; save coordinates every 0
>> nstvout = 100000 ; save velocities every 0
>> 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 = 0.3479 ; short-range neighborlist
>> (in nm)
>> rcoulomb = 0.3479 ; 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 = no;Parrinello-Rahman
>> Pcoupltype = Isotropic
>> tau_p = 1.0
>> compressibility = 6.2e-5
>> ref_p = 50.0
>> gen_vel = yes
>> gen_temp = 179.8
>> gen_seed = 712349
>> DispCorr =no; EnerPres ; account for cut-off vdW
>> constraints = all-bonds ; all bonds constrained (fixed
>> 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
>> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>>>> I get this error only in NVT equlibration step, not in the NPT and
>>>> production steps. Should I worry about it?
>>>> In gromacs page it tell the error can come from 4 reasons, but how I can
>>>> recognize which can be mine?
>>>> Check the size of your largest charge group, value of rlist, or whether
>>> or not the input configuration is "broken" across PBC.
>>>> 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
>>> Gromacs Users mailing list
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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