<div dir="ltr">I want to relax the guanine molecule but the relaxed structure show some hydrogens detached from the main structure (see graph attached). It looks like there is some sort of interaction between the periodic image even I put it in a big box. Please, I will appreciate any suggestions.<div>
<br></div><div><div>Wudmir</div><div>PhD student, UK.</div></div><div>- - - - - - - - - - - - - - - - - - - - - - - - Input - - - - - - - - - - - - -</div><div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">&CONTROL</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> title = ' guanine ',</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> calculation = 'relax',</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> restart_mode = 'from_scratch',</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> tprnfor = .TRUE.,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> etot_conv_thr = 1.D-4,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> prefix = 'gua-relax-22-06-a'</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> pseudo_dir = '~/espresso-pseudo/'</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> outdir = './'</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">&SYSTEM</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> ibrav = 0, </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> celldm(1) = 18.897259886, </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> nat = 16,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> ntyp = 4</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> ecutwfc = 25.0,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> ecutrho = 200.0,</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> occupations='smearing', </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> smearing='gaussian',</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> degauss=0.01</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">/</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"> </span><span style="color:black;font-family:'Menlo Regular';font-size:11pt">&ELECTRONS</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">/</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span><span style="color:black;font-family:'Menlo Regular';font-size:11pt">&IONS</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">/</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span><span style="color:black;font-family:'Menlo Regular';font-size:11pt">ATOMIC_SPECIES</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 12.0107
C.pbe-mt_fhi.UPF</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">O 15.9994
O.pbe-mt_fhi.UPF</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H 1.00794
H.pbe-mt_fhi.UPF</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 14.0067
N.pbe-mt_fhi.UPF</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">K_POINTS gamma</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">CELL_PARAMETERS
(alat)</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> 8.000
0.000 0.00</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> 0.000
8.000 0.00</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> 0.000 0.000
8.00</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black"> </span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">ATOMIC_POSITIONS
(angstrom)</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 0
0 0</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 0
0 1.440908</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 1.357081
0 1.91969</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 2.396462
0 0.987468</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 2.338369
0 -0.36805</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 1.102405
0 -0.817435</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 0.886377
0 -2.16208</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 1.849196
0 3.211795</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">C 3.148326
0 3.067635</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">N 3.542068
0 1.739303</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H -0.032303 0
-2.567841</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H 1.694052
0 -2.761628</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H -0.932932
0 -0.393625</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">O -1.065793
0 2.031419</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H 3.871687
0 3.871397</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:'Menlo Regular';color:black">H 4.482237 0
1.373635</span></p>
</div></div>