Dear all,
I know several questions about implict solvent have already been asked in this
list. I think and hope the question I have has not been raised. Forgive me if I
am wrong.
I have read that all-to-all kernels are the best option when doing implicit
solvent. Otherwise one should use large cutoffs.
I wanto to simulate a tetramer which has more than 1200 residues. I'm afraid
all-to-all interactions are much too expensive in this case. So I should use
largecutoffs. My question is, how large? Or, to be more precise, what should I
monitor to check the the cutoffs are large enough?
As an extra questions, if I don't use all-to-all kernels, is it still worth
using the GPU to accelerate the calculation?
Thanks in advance,
Ramon
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