[gmx-developers] PBC Bug for Triclinic Box in GMX 5.1.4?

[Berk Hess]

Hi,

I think GROMACS is correct. The distances between your atoms are longer 
than half of two of the box vector lengths, so it's very difficult to 
see what the closest periodic image is.
It looks like the real issue is that you forgot to put bonds in your 
topology.

Cheers,

Berk

On 04/20/2017 09:00 PM, Jicun LI wrote:
> Hi,
>
> It seems to me there is a bug in GMX 5.1.4 when calculating the angles 
> in a triclinic box. For some special cases GMX does not apply the PBC 
> well. For example, the HOH angle of the following configuration is 
> about 2 degree, but both `mdrun` and `gangle` will give about 89 degree.
>
> Generated by trjconv : SOL t= 0.00900
>     3
>     1SOL      H    1   0.063   0.448   0.045  9.3129-17.0644  4.3188
>     1SOL      O    2   0.746   0.604   0.203-23.5642 10.7484 10.1804
>     1SOL      H    3   0.059   0.435   0.056 14.2513  6.3160-14.4992
>    1.04000   0.60975   0.52565   0.00000   0.00000  -0.28175 0.00000 
>  -0.28063  -0.01980
>
> Any advice or suggestions will be appreciated. If anyone wants to 
> repeat the results, please use the following input files:
>
> - `conf.gro`
>
> Ang
>    3
>      SOL     H     1   0.270  -0.034   0.016
>      SOL     O     2   0.175  -0.092   0.123
>      SOL     H     3   0.229  -0.217   0.165
>    1.04000   0.60975   0.52565 0.00000   0.00000  -0.28175 0.00000 
>  -0.28063  -0.01980
>
> - `topol.top`
>
> [ defaults ]
> ; nbfunc      comb-rule       gen-pairs fudgeLJ fudgeQQ
> 1               2               yes             1     1
>
> [ atomtypes ]
> ;name   bond_type     mass     charge ptype   sigma epsilon
>  O       O          0.00000  0.00000   A    0 0
>  H       H          0.00000  0.00000   A    0 0
>
> [ moleculetype ]
> ;name nrexcl
>  SOL               3
>
> [ atoms ]
> ; nr  type resi  res  atom cgnr     charge      mass
>     1   H     1   SOL    H    1   0 1
>     2   O     1   SOL    O    2   0 1
>     3   H     1   SOL    H    3   0 1
>
> [ angles ]
> ; ai aj ak funct   theta cth
>      1     2      3      1    1.0750e+01    5.8576e+02
> [ system ]
>  SOL
>
> [ molecules ]
> ; Compound nmols
>  SOL               1
>
> - `grompp.mdp`
>
> integrator               = md
> dt             = 0.001
> tinit              = 0
> nsteps             = 10
> nstcomm              = 1
>
> nstxout              = 1
> nstvout              = 1
> nstfout              = 1
> nstxtcout              = 1
> nstenergy              = 1
> nstlog             = 1
>
> nstlist              = 1
> ns_type              = grid
> pbc              = xyz
>
> rlist    = .2
> rcoulomb = .2
>
> coulombtype              = PME
> fourier-nx = 80
> fourier-ny = 80
> fourier-nz = 80
> pme-order              = 12
> ewald_rtol   = 1E-9
>
> rvdw=0.2
> vdw-type             = Cut-off
>
> tcoupl             = nose-hoover
> tc-grps      = system
> tau_t                    = 2
> ref_t                    = 298.15
>
> gen_vel              = no
> gen_temp                 = 298.15
>
> - `index.ndx`
>
> [ System ]
>    1    2    3
> [ SOL ]
>    1    2    3
> [ ang ]
> 1 2 3
>
> For a 10 steps running, the output of `gangle` I got is
>
> # Command line:
> # gmx gangle -f -n -oall
> # gmx gangle is part of G R O M A C S:
> #
> # Good gRace! Old Maple Actually Chews Slate
> #
> @    title "Angle"
> @ xaxis  label "Time (ps)"
> @ yaxis  label "Angle (degrees)"
> @TYPE xy
>       0.000  107.495
>       0.001   96.084
>       0.002   78.024
>       0.003   59.745
>       0.004   43.710
>       0.005   30.884
>       0.006   20.977
>       0.007   13.337
>       0.008    7.200
>       0.009   89.133
>       0.010    0.907
>
> The angle of 0.009 ps is not correct, in my opinion.
>
> Regards,
> Jicun
>
>

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