GROMACS modification: Yes/No
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I want to perform a simulation for 10 ns. After that, I want to cleave a bond between two DNA residues and continue the simulation. Is it possible? May I face any problems regarding the topology file or anything else?
Does the cleavage involve adding/removing atoms? If so, this might be the hardest part, as you need to dynamically add the atoms to the termini and switch to a different topology.
Either way, removing a bond will require changes to the topology file (can be done either manually or with gromologist, but you still might need to adjust the charges on the cleaved residues) and perhaps a short energy minimization, as the formerly bonded atoms will now be way closer than their non-bonded parameters would allow them to.
Thank you so much. Can I continue the simulation without minimization?
My guess is the simulation will explode or otherwise break down, and even if it doesn’t, there’s always a risk of terminal sugars e.g. changing chirality while atoms bounce around initially. So even a short one, say 20-50 steps, will safeguard you against possibly hard-to-track artifacts. Feel free to try, but just to be safe I wouldn’t do it in the actual production run.
An intermediate strategy would be to initially keep a (semi-harmonic) restraint between the terminal atoms that lost the bond, and then remove it, either by changing the force constant or increasing the allowed distance.
thank you so much