GROMACS version: 2023.3
GROMACS modification: No
Hi everyone!
I have problems with DNA modeling. During molecular dynamics, DNA loses nucleotide bonds. Upon closer examination, literally one connection is missing. It disappears during the molecular dynamics ensemble.
Does anyone know what could be wrong? I still can’t determine the reason. Maybe it’s something to do with the dos2unix program? Or in .mdp files?
Please, help. I spent a lot of time on this.
Thanks!
Bonds cannot break or form during molecular mechanical processes. Either the bond is there or it isn’t in the topology. Do not trust what VMD (or any other visualization program) show you with respect to bonded connectivity; they are all guesses based on ideal bond lengths. They usually do a very good job but they are not definitive. The topology is.
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Thanks for the reply.
Here the screen of NPT.gro ensemble. Topology have no problems.
What could I do to avoid such problem?
This started happening quite recently. Maybe it’s something to do with the VMD settings?
Maybe there are some analogues of VMD?
This is not a problem with VMD. If your initial frame has “strange” bond lengths, VMD will not see them as bonds (unless there are CONECT entries in the PDB, but that’s uncommon), therefore to avoid visualization artifacts, load an energy-minimized frame first alongside the trajectory. For actual validation, check the [ bonds ] section of your topology file.
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Thanks, this should help.