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

[Jicun LI]

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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