Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am just using the lipid bilayer)?
After the script is run, When I try doing the energy minimization, it shows unequal number of atoms in .gro and topology file. (the GRO Input has only lipid molecules where as topology files takes into account both SOL and lipid molecules). How to remove this error? I am unable to find any tutorial that could guide through the steps and the parameters to be set while doing the simulation of only bilayers. Please suggest some tutorial. Kindly guide through the steps. Regards, Saumya
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