What is the difference in hamiltonians between neighboring replicas? You
mention reaction coordinate, are you changing the position of a harmonic
restraint? If yes, then the force constant is also important in addition to
spacing.
Look at the energy difference reported in the output you sent, it is very
large. Does that make sense? Setting up these simulations can be tricky,
and needs information that only you know. It also takes a good
understanding of the principles behind HREMD, and how the exchange works.
You might start by calculating the reaction coordinate value vs time for
each replica, making a histogram, and seeing if they have overlap.
On Fri, Sep 20, 2024, 4:34 PM Liyanage, Risi (MU-Student) via AMBER <
amber.ambermd.org> wrote:
> Dear amber community,
>
> I am trying to run a h-remd for a relatively large system (60404 atoms
> after solvation). To create the replicas i have changed the distance
> between CoMs of two residues (as the reaction coordinate) and picked
> replicas from that. I have conducted the same simulation for a smaller
> system (setting 0.6 Angstrom reaction coordinate difference between each
> replica) and did not encounter any issues. But for the larger system I have
> tried, 0.1,0.2,0.3,0.4 angstrom differences but still not getting any
> replica exchanges. Infact left_fe, right_fe keep showing '-infinity'
> (picture attached). Since h-remd is said to be less dependent on the number
> of replicas (as opposed to t-remd) with the increasing system size, this
> problem is quite difficult for me to understand. Can anyone give me an idea
> about this issue or propose a way to calculate the number of replicas for
> h-remd?
>
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Received on Sat Sep 21 2024 - 05:00:02 PDT
