<div dir="ltr">P.S. I'd like to use this as a way to recognise a OH- ion in solution. It seems to work when I have to identify the highest coordinated atom to say 235 in the example. But I'd like to identify lowest coordinated atom (the OH- ion) and then use this to compute the distance between this atom and atom 235. I'm not sure if this CV can be used to do that<div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Nov 13, 2016 at 1:24 AM, Nitish Govindarajan <span dir="ltr"><<a href="mailto:gnitis...@gmail.com" target="_blank">gnitis...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks a lot for your reply marcella. I changed the parameters but I still find that after the first SCF cycle, the output just hangs. So I'm not sure what is wrong.<div><br></div><div>Thanks</div><span class="HOEnZb"><font color="#888888"><div>Nitish</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Nov 12, 2016 at 12:27 PM, Marcella Iannuzzi <span dir="ltr"><<a href="mailto:marci...@gmail.com" target="_blank">marci...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nitish,<div><br></div><div>yes this variable has been successfully used. </div><div>It is meant to calculate the distance between one atom and one atom taken from another group of atoms.</div><div>To select the second atom, the coordination function is selected, i.e., the atom with the largest coordination number is selected.</div><div>Using an input like</div><div><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> &COLVAR</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> &CONDITIONED_DISTANCE</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> ATOMS_DISTANCE 235</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> KINDS_FROM N</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> ATOMS_TO 235</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> R0 [angstrom] 3.00000000E+00</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> NN 10</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> ND 16</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> LAMBDA 100</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> &END</span></p>
<p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"> &END COLVAR</span></p><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">The distance is calculated between atom 235 and the N atom that has the largest coordination with atom 235, i.e., the closest to atom 235.</span></p><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Kind regards</span></p><span class="m_-3729947613864850823HOEnZb"><font color="#888888"><p style="font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Marcella</span></p></font></span><div><div class="m_-3729947613864850823h5"><br>On Friday, November 11, 2016 at 1:03:03 PM UTC+1, Nitish Govindarajan wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi everyone,<div>I was wondering if anyone has tried using the conditioned distance as a CV in a metadynamics run. I am trying to use this, but I have some questions on how to define ATOMS_DISTANCE and also the output seems to not print after the 1st SCF cycle run.</div><div><br></div><div><p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> &CONDITIONED_DISTANCE</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 2</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 3</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 4</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 5</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 7</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 8</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 9</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 10</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 11</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 12</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 13</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 14</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 15</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ATOMS_DISTANCE 6 16</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> KINDS_FROM O</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> KINDS_TO </span><span style="background-color:#e6e600">H</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> LAMBDA -20</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> ND 32</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> NN 8</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> R0 [angstrom] 1.27</span></p>
<p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span> &END CONDITIONED_DISTANCE</span></p><p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span><br></span></p><p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span>Thanks,</span></p><p style="font-size:22px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Nitish</p></div></div></blockquote></div></div></div></div><div class="m_-3729947613864850823HOEnZb"><div class="m_-3729947613864850823h5">
<p></p>
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