[gmx-users] Implicit solvent setup for large protein
Ramon Crehuet Simon
rcsqtc at cid.csic.es
Tue Jul 3 14:57:55 CEST 2012
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,
More information about the gromacs.org_gmx-users