[gmx-users] Implicit solvent setup for large protein

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 3 15:01:12 CEST 2012

On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote:
> 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?

In my experience, using long cutoffs leads to unstable trajectories and very 
poor energy conservation.  The all-vs-all kernels are the only ones I use for 
implicit calculations.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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