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

[Jicun LI]

Hi Berk,

Thanks for your comments. Do you know the method GMX used to apply PBC for
triclinic box? There are different approaches for this problem, but I think
only the method using inverted cell matrix will be correct for any cases.
Please look at https://scicomp.stackexchange
.com/questions/3107/minimum-image-convention-for-triclinic-unit-cell. For
my case, I did not put bonds in my topology, otherwise the angle will not
change dramatically and GMX may not encounter the problems.

Regards,
Jicun

2017-04-20 14:51 GMT-05:00 Berk Hess <hess at kth.se>:

> 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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