<div dir="ltr">Hi Reza,<div><br></div><div>This mailing list is intended for development/code discussion, not getting usage support. Please use the forums instead.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jan 6, 2022 at 5:58 PM reza.khabani <<a href="mailto:reza.khabani@ut.ac.ir">reza.khabani@ut.ac.ir</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="font-size:10pt;font-family:Verdana,Geneva,sans-serif">
<blockquote type="cite" style="padding:0px 0.4em;border-left-width:2px;border-left-style:solid;border-left-color:rgb(16,16,255);margin:0px">
<p style="text-align:justify">Dear Developer of Gromacs,</p>
<p style="text-align:justify">I want to calculate energy binding with the LIE method in Gromacs, but Gromacs 2021 cannot read the energy file correctly (ener.edr). For this purpose, I will explain the simulation step by step so that if there is a problem, help me solve this problem. CNT and inhibitor molecules are simulated in water. An additional simulation (Inhibitor in water) is required to calculate energy binding with the LIE method. According to the Gromacs Manual, I went through all the steps as follows:</p>
<ol style="text-align:justify">
<li>Add in .mdp file "energygrps = CNT inhibitor" (in CNT-inhibitor-Water simulation)</li>
<li>Add in .mdp file "energygrps = inhibitor SOL" (in inhibitor-Water simulation)</li>
<li>The following commands were executed to simulate the inhibitor-Water:</li>
</ol>
<p style="text-align:justify">gmx grompp -f binding_energy2.mdp -c run.gro -p topol.top -o binding.tpr -maxwarn 13</p>
<p style="text-align:justify">gmx mdrun -s binding.tpr -rerun run.xtc –nb cpu –deffnm ener2</p>
<p style="text-align:justify">gmx energy -f ener2.edr -o bindingenergy.xvg -b 9000 > binding.log</p>
<p style="text-align:justify">Select the inhibitor-SOL option</p>
<p style="text-align:justify">Elj=29.338 ,Eqq=-419.446</p>
<ol style="text-align:justify">
<li>The following commands were executed to simulate the CNT-inhibitor-Water:</li>
</ol>
<p style="text-align:justify">gmx grompp -f binding_energy1.mdp -c run.gro -p topol.top -o binding.tpr -maxwarn 13</p>
<p style="text-align:justify">gmx mdrun -s binding.tpr -rerun run.xtc –nb cpu –deffnm ener</p>
<ol style="text-align:justify">
<li>The “gmx lie” command was used to calculate energy binding in the last step.</li>
</ol>
<p style="text-align:justify">gmx lie -f ener.edr -b 9000 -Elj 29.338 -Eqq -419.446 -ligand inhibitor -o lie.xvg</p>
<p style="text-align:justify">At this point,<span> </span><strong>Gromacs cannot extract the relevant data from the ener.edr file and the numbers it reports are unrealistic and incorrect</strong>. Thank you for helping me solve this problem.</p>
<p style="text-align:justify"> </p>
<p>I wish you all the best,</p>
<p>Reza Khiabani</p>
<div> </div>
</blockquote>
<p><br></p>
</div>
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