I want to generate a trajectory using my MD data that only contains solvent and solutes that are smaller than the 0.35 limit. I make the index file of those residue. From one frame to the next, however, it changed in the solvent molecule within cutoff. so that this is not a good idea. Could someone kindly offer some tips on how to do it in Gromacs?
Ashkan Zare Karizak
I appreciate your suggestion. Whatever you say, I already did. The solvent molecule does not adhere to the solute molecule's surface. Following the first snapshot, it departs and another solvent molecule enters. Only one snapshot can be used to create and retain an index file. Therefore, for every snapshot of the trajectory, I want the solute and solvent molecules to be inside the cutoff of 0.35 nm.
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