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<div class="moz-cite-prefix">Hi,<br>
<br>
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.<br>
It looks like the real issue is that you forgot to put bonds in
your topology.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 04/20/2017 09:00 PM, Jicun LI wrote:<br>
</div>
<blockquote
cite="mid:CALHrUYvixyRKh5csC7kPjjmYxG3aqSmAfrOa7RPrX257gH0F_Q@mail.gmail.com"
type="cite">
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<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 "Angle"<br>
@ <span class="" id=":2o4.234" tabindex="-1">xaxis</span>
label "Time (<span class="" id=":2o4.235" tabindex="-1">ps</span>)"<br>
@ <span class="" id=":2o4.236" tabindex="-1">yaxis</span>
label "Angle (degrees)"<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>
<br>
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