<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><p style="font-size: 11px; line-height: normal; font-family: Menlo;"><span style="font-variant-ligatures: no-common-ligatures">Marcella</span></p><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>