<div dir="ltr">Hi,<br><br>It seems to me there is a bug in <span class="" id=":2o4.161" tabindex="-1">GMX</span> 5.1.4 when calculating the angles in a <span class="" id=":2o4.162" tabindex="-1">triclinic</span> box. For some special cases <span class="" id=":2o4.163" tabindex="-1">GMX</span> does not apply the <span class="" id=":2o4.164" tabindex="-1">PBC</span> well. For example, the <span class="" id=":2o4.165" tabindex="-1">HOH</span> angle of the following configuration is about 2 degree, but both `<span class="" id=":2o4.166" tabindex="-1">mdrun</span>` and `<span class="" id=":2o4.167" tabindex="-1">gangle</span>` will give about 89 degree.<br><br><font face="monospace, monospace">Generated by <span class="" id=":2o4.168" tabindex="-1">trjconv</span> : SOL t=   0.00900<br>    3<br>    1SOL      H    1   0.063   0.448   0.045  9.3129-17.0644  4.3188<br>    1SOL      O    2   0.746   0.604   0.203-23.5642 10.7484 10.1804<br>    1SOL      H    3   0.059   0.435   0.056 14.2513  6.3160-14.4992<br>   1.04000   0.60975   0.52565   0.00000   0.00000  -0.28175   0.00000  -0.28063  -0.01980</font><br><br>Any advice or suggestions will be appreciated. If anyone wants to repeat the results, please use the following input files:<br><br>- `<span class="" id=":2o4.169" tabindex="-1">conf</span>.<span class="" id=":2o4.170" tabindex="-1">gro</span>`<br><br><font face="monospace, monospace"><span class="" id=":2o4.171" tabindex="-1">Ang</span><br>   3<br>     SOL     H     1   0.270  -0.034   0.016<br>     SOL     O     2   0.175  -0.092   0.123<br>     SOL     H     3   0.229  -0.217   0.165<br>   1.04000   0.60975   0.52565 0.00000   0.00000  -0.28175   0.00000  -0.28063  -0.01980</font><br><br>- `<span class="" id=":2o4.172" tabindex="-1">topol</span>.top`<br><br><font face="monospace, monospace">[ defaults ]<br>; <span class="" id=":2o4.173" tabindex="-1">nbfunc</span>        comb-rule       gen-pairs       <span class="" id=":2o4.174" tabindex="-1">fudgeLJ</span> <span class="" id=":2o4.175" tabindex="-1">fudgeQQ</span><br>1               2               yes             1     1<br><br>[ <span class="" id=":2o4.176" tabindex="-1">atomtypes</span> ]<br>;name   bond_type     mass     charge   <span class="" id=":2o4.177" tabindex="-1">ptype</span>   sigma         epsilon<br> O       O          0.00000  0.00000   A    0 0<br> H       H          0.00000  0.00000   A    0 0<br><br>[ <span class="" id=":2o4.178" tabindex="-1">moleculetype</span> ]<br>;name            <span class="" id=":2o4.179" tabindex="-1">nrexcl</span><br> SOL               3<br><br>[ atoms ]<br>;   <span class="" id=":2o4.180" tabindex="-1">nr</span>  type  <span class="" id=":2o4.181" tabindex="-1">resi</span>  res  atom  <span class="" id=":2o4.182" tabindex="-1">cgnr</span>     charge      mass<br>    1   H     1   SOL    H    1   0 1<br>    2   O     1   SOL    O    2   0 1<br>    3   H     1   SOL    H    3   0 1<br><br>[ angles ]<br>;   <span class="" id=":2o4.183" tabindex="-1">ai</span>     <span class="" id=":2o4.184" tabindex="-1">aj</span>     <span class="" id=":2o4.185" tabindex="-1">ak</span>    <span class="" id=":2o4.186" tabindex="-1">funct</span>   theta         <span class="" id=":2o4.187" tabindex="-1">cth</span><br>     1     2      3      1    1.0750e+01    5.8576e+02<br>[ system ]<br> SOL<br><br>[ molecules ]<br>; Compound        <span class="" id=":2o4.188" tabindex="-1">nmols</span><br> SOL               1<br></font><br>- `<span class="" id=":2o4.189" tabindex="-1">grompp</span>.<span class="" id=":2o4.190" tabindex="-1">mdp</span>`<br><br><font face="monospace, monospace">integrator               = <span class="" id=":2o4.191" tabindex="-1">md</span><br><span class="" id=":2o4.192" tabindex="-1">dt</span>                       = 0.001<br><span class="" id=":2o4.193" tabindex="-1">tinit</span>                    = 0<br><span class="" id=":2o4.194" tabindex="-1">nsteps</span>                   = 10<br><span class="" id=":2o4.195" tabindex="-1">nstcomm</span>                  = 1<br><br><span class="" id=":2o4.196" tabindex="-1">nstxout</span>                  = 1<br><span class="" id=":2o4.197" tabindex="-1">nstvout</span>                  = 1<br><span class="" id=":2o4.198" tabindex="-1">nstfout</span>                  = 1<br><span class="" id=":2o4.199" tabindex="-1">nstxtcout</span>                = 1<br><span class="" id=":2o4.200" tabindex="-1">nstenergy</span>                = 1<br><span class="" id=":2o4.201" tabindex="-1">nstlog</span>                   = 1<br><br><span class="" id=":2o4.202" tabindex="-1">nstlist</span>                  = 1<br><span class="" id=":2o4.203" tabindex="-1">ns</span>_type                  = grid<br><span class="" id=":2o4.204" tabindex="-1">pbc</span>                      = <span class="" id=":2o4.205" tabindex="-1">xyz</span><br><br><span class="" id=":2o4.206" tabindex="-1">rlist</span>    = .2<br><span class="" id=":2o4.207" tabindex="-1">rcoulomb</span> = .2<br><br><span class="" id=":2o4.208" tabindex="-1">coulombtype</span>              = <span class="" id=":2o4.209" tabindex="-1">PME</span><br><span class="" id=":2o4.210" tabindex="-1">fourier</span>-<span class="" id=":2o4.211" tabindex="-1">nx</span>               = 80<br><span class="" id=":2o4.212" tabindex="-1">fourier</span>-<span class="" id=":2o4.213" tabindex="-1">ny</span>               = 80<br><span class="" id=":2o4.214" tabindex="-1">fourier</span>-<span class="" id=":2o4.215" tabindex="-1">nz</span>               = 80<br><span class="" id=":2o4.216" tabindex="-1">pme</span>-order                = 12<br><span class="" id=":2o4.217" tabindex="-1">ewald</span>_<span class="" id=":2o4.218" tabindex="-1">rtol</span>               = 1E-9<br><br><span class="" id=":2o4.219" tabindex="-1">rvdw</span>=0.2<br><span class="" id=":2o4.220" tabindex="-1">vdw</span>-type                 = Cut-off<br><br><span class="" id=":2o4.221" tabindex="-1">tcoupl</span>                   = nose-hoover<br><span class="" id=":2o4.222" tabindex="-1">tc</span>-<span class="" id=":2o4.223" tabindex="-1">grps</span>                  = system<br>tau_t                    = 2<br>ref_t                    = 298.15<br><br>gen_<span class="" id=":2o4.224" tabindex="-1">vel</span>                  = no<br>gen_temp                 = 298.15</font><br><br>- `index.<span class="" id=":2o4.225" tabindex="-1">ndx</span>`<br><br><font face="monospace, monospace">[ System ]<br>   1    2    3<br>[ SOL ]<br>   1    2    3<br>[ <span class="" id=":2o4.226" tabindex="-1">ang</span> ]<br>1 2 3</font><br><br>For a 10 steps running, the output of `<span class="" id=":2o4.227" tabindex="-1">gangle</span>` I got is<br><br><font face="monospace, monospace"># Command line:<br>#   <span class="" id=":2o4.228" tabindex="-1">gmx</span> <span class="" id=":2o4.229" tabindex="-1">gangle</span> -f -n -<span class="" id=":2o4.230" tabindex="-1">oall</span><br># <span class="" id=":2o4.231" tabindex="-1">gmx</span> <span class="" id=":2o4.232" tabindex="-1">gangle</span> is part of G R O M A C S:<br>#<br># Good <span class="" id=":2o4.233" tabindex="-1">gRace</span>! Old Maple Actually Chews Slate<br>#<br>@    title &quot;Angle&quot;<br>@    <span class="" id=":2o4.234" tabindex="-1">xaxis</span>  label &quot;Time (<span class="" id=":2o4.235" tabindex="-1">ps</span>)&quot;<br>@    <span class="" id=":2o4.236" tabindex="-1">yaxis</span>  label &quot;Angle (degrees)&quot;<br>@TYPE <span class="" id=":2o4.237" tabindex="-1">xy</span><br>      0.000  107.495<br>      0.001   96.084<br>      0.002   78.024<br>      0.003   59.745<br>      0.004   43.710<br>      0.005   30.884<br>      0.006   20.977<br>      0.007   13.337<br>      0.008    7.200<br>      0.009   89.133<br>      0.010    0.907</font><br><br>The angle of 0.009 <span class="" id=":2o4.238" tabindex="-1">ps</span> is not correct, in my opinion.<br> <br>Regards,<br><span class="" id=":2o4.239" tabindex="-1">Jicun</span></div>