From: Victor Zhao (yzhao01_at_g.harvard.edu)
Date: Mon Jan 25 2021 - 16:26:23 CST
Dear Brian,
It is possible to rewrite the trajectories so that you have trajectories by replica rung. The sortreplicas script included with NAMD does that. I am asking about RMSF computed over a single rung, which would be made up of many individual trajectories as they passed through that rung.
Best regards,
Victor
> On Jan 25, 2021, at 5:22 PM, Brian Radak <brian.radak_at_gmail.com> wrote:
>
> Hi Victor,
>
> How you calculate any observable (including RMSF) with replica exchange depends on the implementation. I'm pretty sure (although I might be wrong) that all of the REMD scripts distributed with NAMD track replicas (i.e. the state parameter, here the REST2 "temperature", changes over the course of the trajectory).
>
> In this case, the RMSF should be the same over all trajectories within statistical uncertainty. This also means that:
>
> 1. The trajectory statistics can be pooled under the assumption that they are independent
>
> 2. Any differences across trajectories are entirely sampling artifacts.
>
> I would also contend that the RMSF computed this way is a completely unphysical quantity that only gives you an impression of sampling efficiency. It does not even describe real population thermodynamics. For that you would have to apply a WHAM-like scheme. I don't know if any scripts for that purpose are readily available.
>
> HTH,
>
> BKR
>
>
>
> On 1/25/21 4:50 PM, Victor Zhao wrote:
>> Dear all,
>>
>> I have been running replica exchange simulations (REST2). So far, I have focused on observables calculated on a per-frame basis and averaged to obtain ensemble values. But I am wondering, is it useful to calculate RMSF in a replica exchange simulation? Presumably you would do it over the replica index of interest (i.e. replica 0). But the trajectory at each replica setting includes exchanges between replicas. And yet I’ve read papers where RMSF is still calculated in replica exchange simulations.
>>
>> Often, RMSF calculations presented in papers don’t appear to make a larger point beyond that different parts of the protein differ in flexibility, so I think RMSF calculations in a replica exchange simulation could serve the same purpose. But when it comes to the issue of comparing RMSF between different replica exchange simulations, wouldn’t different exchange acceptance rates prevent comparison between simulations? That is, suppose one simulation has a 0 <-> 1 exchange rate of 0.2 whereas another has an exchange rate of 0.25. In this case, the average time between exchanges would be different, which could affect RMSF. I am wondering what the experts on this list think.
>>
>> Best regards,
>>
>> Victor Zhao
>> PhD Candidate, Chemistry
>> Shakhnovich Lab, Harvard University
>> yzhao01_at_g.harvard.edu <mailto:yzhao01_at_g.harvard.edu>
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