[gmx-users] The sum of the two largest charge group radii (X) is larger than rlist
fpoosaneh at gmail.com
Sun Dec 17 14:22:51 CET 2017
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.
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 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 = 0.3479 ; short-range neighborlist cutoff
> (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
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