Dear Gromacs users, I'd like to perform a simulation following the protocol applied in the Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ).
In particular, I refer to some topic details reported here: *...The MD simulation was performed using [...] CHARMM 32a216 [...] 15 attempts to generate a MD trajectory without applying nuclear Overhauser enhancement (NOE) restraints led to a loss of the secondary structure of TM7. For this reason the first 5 ns of the MD were performed with the NOE restraints applied for the distances between the backbone carbonyl oxygen atom of the residue n and the backbone NH-group of the residue n+4 of TM7[...]The restraints were applied to all the residues, with the exception of the prolines and residues immediately following [...]That constraint preserved the helical structure of TM7, which remained stable after removing the NOE restraints. [...] After 5 ns the MD simulation was continued without any restraints...* How can I do it with Gromacs? I suppose that I also could manually provide classical distance restraints, defining arbitrary Hbond cutoffs instead of NOE distance restraints, but a such alternative sounds less elegant to me. Any suggestion will be greatly appreciated! Thanks in advance, Chiara
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