Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks.
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