While generating the initial coordinate and topology files for DNA simulation in water, we add counter ions to neutralize the backbone charge. I use leap (AMBERTOOLS) to solvate and add ions. But I am little puzzled whether to add ions then solvate or first solvate then add ions. I found that research articles on DNA simulation are not very strict to the order, some article first solvate and then add ions, others do vice-versa.
Does the sequence of solvation and ion adding not matter. If it does then which is the correct one.
Hi Himanshu... Please take it as a discussion rather than an answer to your question. First of all, when we add water and then add ions using LEaP, the code removes a water molecule whenever it overlaps with the ion being added. If the reverse is done then this removal won't happen even in case of an overlap (Please correct me if I am wrong here). This might be fine for mildly charged systems. But simulating densely charged systems like DNA and some other bio-molecules by adding ions first and then adding water may lead to large number of such overlaps, which may or may not get removed during a finite number of minimization steps. The problem may be larger when the simulation needs to be performed at a given non-zero molarity.
Secondly, if ions are added first, then while adding water with a given value of solvation shell, the code would calculate the distance from the farthest ion in any given direction rather than a solute atom. Again, in case of small and mildly charged systems, this may not be a problem, but in case of large systems with dense charges (and extra ions added to achieve a given value of molarity), the protocol of adding ions first may give rise to uselessly larger systems.
What do you think? Did you find anything regarding this? If yes, please share.
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