Hi Amber users,
I have been running MD simulations with biomolecules (DNA.BSC1 force field
) using Amber 18.
The resultant trajectories often have short intermolecular hydrogen bonds
(2.4 - 2.6 A) between solute molecules and the solvent (water). Later, when
I perform QM calculations on these systems, it often causes problems.
I have tried distance restraints, but they did not work properly as there
were many of them, and due to other complications.
Please let me know if you have any suggestions to avoid this problem.
Your help is much appreciated.
Thanks,
--
Siddhique
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Received on Tue Jul 04 2023 - 08:00:02 PDT
