Amber Users,
I am preparing to run a Partial Nudged Elastic Band simulation on a nucleic
acid molecule that has two very different conformations. I will be running
this simulation in explicit solvent. I am encountering a problem that the
two .prmtop files created for each endpoint of the simulation are different.
I have added counter ions and solvated each endpoint conformation using a
TIP3PBOX. As expected due to the identical charge and large difference in
conformation, each conformation had the same number of counter ions but a
different number of water molecules. Since both conformations have the same
number and identity of solute atoms, I assume that the difference in the
.prmtop files stems from the unequal amount of water (solvent) molecules for
each.
Is this a correct assumption?
If this is correct, do I stand to create any artifacts in my simulation by
simply using the .prmtop file that contains the larger octahedral water box?
Thank you in advance for your help!
Adieu,
Will Cantara
Graduate Student, North Carolina State University
Research Project Asst., The RNA Institute, SUNY Albany
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Received on Fri Aug 12 2011 - 06:00:02 PDT
