Hello Jason,
The number of replicas required to cover a given temperature range increases with the total number of atoms. Therefore, for a system as large as yours (and mainly in explicit solvent) T-REMD becomes impractical because the number of replicas required for a reasonable exchange rate would have to be very large.
In order to check if a given distribution of temperatures is good, you can run a short simulation and check your rem.log file.
I have seen publications in which people use Hamiltonian-REMD instead of T-REMD for large system in order to have a good and efficient temperature sampling. I know they scale the Hamiltonian of each replica to a different effective temperature in order to mimic what happens in T-REMD and good exchange rates are obtained and with a reasonable number of replicas. I have never done calculations like this before though, therefore I don’t know the technical details.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Mar 21, 2018, at 6:16 PM, Jason Ku Wang <jwang198.stanford.edu<mailto:jwang198.stanford.edu>> wrote:
Hi AMBER community!
I'm interested in running temperature-based replica exchange for a soluble
protein of ~140,000 atoms in a periodic box with explicit solvent.
I'm having trouble determining the number of replicas and the corresponding
temperature distribution. Are there any resources/protocols that you have
found helpful for determining the temperature distribution?
Furthermore, how does one know that a given temperature distribution is a
good one?
Thanks in advance!
Jason
--
Jason Wang
Stanford University, Class of 2018
jwang198.stanford.edu<mailto:
jwang198.stanford.edu>
ᐧ
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Received on Wed Mar 21 2018 - 17:00:02 PDT
