<div dir="ltr">Hi Berk,<div><br></div><div>Thanks for your comments. Do you know the method <span class="" id=":24r.33" tabindex="-1">GMX</span> used to apply <span class="" id=":24r.34" tabindex="-1">PBC</span> for <span class="" id=":24r.35" tabindex="-1">triclinic</span> 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://<span class="" id=":24r.36" tabindex="-1">scicomp</span>.<span class="" id=":24r.37" tabindex="-1">stackexchange</span>.com/questions/3107/minimum-image-convention-for-<span class="" id=":24r.38" tabindex="-1">triclinic</span>-unit-cell. For my case, I did not put bonds in my topology, otherwise the angle will not change dramatically and <span class="" id=":24r.39" tabindex="-1">GMX</span> may not encounter the problems.</div><div><br></div><div>Regards,</div><div><span class="" id=":24r.40" tabindex="-1">Jicun</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-04-20 14:51 GMT-05:00 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div class="m_-39990220479687340moz-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<div><div class="h5"><br>
<br>
On 04/20/2017 09:00 PM, Jicun LI wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi,<br>
<br>
It seems to me there is a bug in <span id="m_-39990220479687340:2o4.161">GMX</span> 5.1.4 when calculating the angles in
a <span id="m_-39990220479687340:2o4.162">triclinic</span>
box. For some special cases <span id="m_-39990220479687340:2o4.163">GMX</span> does not apply the <span id="m_-39990220479687340:2o4.164">PBC</span> well. For example, the
<span id="m_-39990220479687340:2o4.165">HOH</span> angle of
the following configuration is about 2 degree, but both `<span id="m_-39990220479687340:2o4.166">mdrun</span>` and `<span id="m_-39990220479687340:2o4.167">gangle</span>` will give
about 89 degree.<br>
<br>
<font face="monospace, monospace">Generated by <span id="m_-39990220479687340:2o4.168">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 id="m_-39990220479687340:2o4.169">conf</span>.<span id="m_-39990220479687340:2o4.170">gro</span>`<br>
<br>
<font face="monospace, monospace"><span id="m_-39990220479687340:2o4.171">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 id="m_-39990220479687340:2o4.172">topol</span>.top`<br>
<br>
<font face="monospace, monospace">[ defaults ]<br>
; <span id="m_-39990220479687340:2o4.173">nbfunc</span>
comb-rule gen-pairs <span id="m_-39990220479687340:2o4.174">fudgeLJ</span> <span id="m_-39990220479687340:2o4.175">fudgeQQ</span><br>
1 2 yes 1 1<br>
<br>
[ <span id="m_-39990220479687340:2o4.176">atomtypes</span>
]<br>
;name bond_type mass charge <span id="m_-39990220479687340:2o4.177">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 id="m_-39990220479687340:2o4.178">moleculetype</span>
]<br>
;name <span id="m_-39990220479687340:2o4.179">nrexcl</span><br>
SOL 3<br>
<br>
[ atoms ]<br>
; <span id="m_-39990220479687340:2o4.180">nr</span>
type <span id="m_-39990220479687340:2o4.181">resi</span>
res atom <span id="m_-39990220479687340:2o4.182">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 id="m_-39990220479687340:2o4.183">ai</span>
<span id="m_-39990220479687340:2o4.184">aj</span> <span id="m_-39990220479687340:2o4.185">ak</span> <span id="m_-39990220479687340:2o4.186">funct</span> theta
<span id="m_-39990220479687340:2o4.187">cth</span><br>
1 2 3 1 1.0750e+01 5.8576e+02<br>
[ system ]<br>
SOL<br>
<br>
[ molecules ]<br>
; Compound <span id="m_-39990220479687340:2o4.188">nmols</span><br>
SOL 1<br>
</font><br>
- `<span id="m_-39990220479687340:2o4.189">grompp</span>.<span id="m_-39990220479687340:2o4.190">mdp</span>`<br>
<br>
<font face="monospace, monospace">integrator = <span id="m_-39990220479687340:2o4.191">md</span><br>
<span id="m_-39990220479687340:2o4.192">dt</span>
= 0.001<br>
<span id="m_-39990220479687340:2o4.193">tinit</span>
= 0<br>
<span id="m_-39990220479687340:2o4.194">nsteps</span>
= 10<br>
<span id="m_-39990220479687340:2o4.195">nstcomm</span>
= 1<br>
<br>
<span id="m_-39990220479687340:2o4.196">nstxout</span>
= 1<br>
<span id="m_-39990220479687340:2o4.197">nstvout</span>
= 1<br>
<span id="m_-39990220479687340:2o4.198">nstfout</span>
= 1<br>
<span id="m_-39990220479687340:2o4.199">nstxtcout</span>
= 1<br>
<span id="m_-39990220479687340:2o4.200">nstenergy</span>
= 1<br>
<span id="m_-39990220479687340:2o4.201">nstlog</span>
= 1<br>
<br>
<span id="m_-39990220479687340:2o4.202">nstlist</span>
= 1<br>
<span id="m_-39990220479687340:2o4.203">ns</span>_type
= grid<br>
<span id="m_-39990220479687340:2o4.204">pbc</span>
= <span id="m_-39990220479687340:2o4.205">xyz</span><br>
<br>
<span id="m_-39990220479687340:2o4.206">rlist</span> =
.2<br>
<span id="m_-39990220479687340:2o4.207">rcoulomb</span> =
.2<br>
<br>
<span id="m_-39990220479687340:2o4.208">coulombtype</span>
= <span id="m_-39990220479687340:2o4.209">PME</span><br>
<span id="m_-39990220479687340:2o4.210">fourier</span>-<span id="m_-39990220479687340:2o4.211">nx</span>
= 80<br>
<span id="m_-39990220479687340:2o4.212">fourier</span>-<span id="m_-39990220479687340:2o4.213">ny</span>
= 80<br>
<span id="m_-39990220479687340:2o4.214">fourier</span>-<span id="m_-39990220479687340:2o4.215">nz</span>
= 80<br>
<span id="m_-39990220479687340:2o4.216">pme</span>-order
= 12<br>
<span id="m_-39990220479687340:2o4.217">ewald</span>_<span id="m_-39990220479687340:2o4.218">rtol</span>
= 1E-9<br>
<br>
<span id="m_-39990220479687340:2o4.219">rvdw</span>=0.2<br>
<span id="m_-39990220479687340:2o4.220">vdw</span>-type
= Cut-off<br>
<br>
<span id="m_-39990220479687340:2o4.221">tcoupl</span>
= nose-hoover<br>
<span id="m_-39990220479687340:2o4.222">tc</span>-<span id="m_-39990220479687340:2o4.223">grps</span>
= system<br>
tau_t = 2<br>
ref_t = 298.15<br>
<br>
gen_<span id="m_-39990220479687340:2o4.224">vel</span>
= no<br>
gen_temp = 298.15</font><br>
<br>
- `index.<span id="m_-39990220479687340:2o4.225">ndx</span>`<br>
<br>
<font face="monospace, monospace">[ System ]<br>
1 2 3<br>
[ SOL ]<br>
1 2 3<br>
[ <span id="m_-39990220479687340:2o4.226">ang</span> ]<br>
1 2 3</font><br>
<br>
For a 10 steps running, the output of `<span id="m_-39990220479687340:2o4.227">gangle</span>` I got is<br>
<br>
<font face="monospace, monospace"># Command line:<br>
# <span id="m_-39990220479687340:2o4.228">gmx</span> <span id="m_-39990220479687340:2o4.229">gangle</span> -f -n -<span id="m_-39990220479687340:2o4.230">oall</span><br>
# <span id="m_-39990220479687340:2o4.231">gmx</span> <span id="m_-39990220479687340:2o4.232">gangle</span> is part
of G R O M A C S:<br>
#<br>
# Good <span id="m_-39990220479687340:2o4.233">gRace</span>!
Old Maple Actually Chews Slate<br>
#<br>
@ title "Angle"<br>
@ <span id="m_-39990220479687340:2o4.234">xaxis</span>
label "Time (<span id="m_-39990220479687340:2o4.235">ps</span>)"<br>
@ <span id="m_-39990220479687340:2o4.236">yaxis</span>
label "Angle (degrees)"<br>
@TYPE <span id="m_-39990220479687340:2o4.237">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 id="m_-39990220479687340:2o4.238">ps</span>
is not correct, in my opinion.<br>
<br>
Regards,<br>
<span id="m_-39990220479687340:2o4.239">Jicun</span></div>
<br>
<fieldset class="m_-39990220479687340mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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