Re: Force and RMSD Values for TMD

From: Vermaas, Josh (
Date: Thu Jun 30 2022 - 16:05:10 CDT

Hi Mukerrem,

I can't comment on TMD too much, but I think not being able to get below 1 angstrom RMSD is very common. The way to think about this that there is literally only 1 conformation that can have exactly 0 RMSD. There are more conformations that have 1 angstrom RMSD from the target, and even more that have 2 angstrom RMSD from the target, and so on. So it gets progressively harder for targeted forces to trap a structure in a given state so long as there is a thermostat in place heating up the system.


On 6/30/22, 4:26 PM, " on behalf of Mükerrem Tüfekçioğlu" < on behalf of> wrote:

    Hi everyone,

    I am working to understand the conformational pathway of a protein that goes between an open to a closed state. I am running 5,000,000-step targeted molecular dynamics simulations with different force and target-RMSD values, but I can never get below RMSD values of 1.0 between the last frame of the simulation and the target structure. Is this to be excepted?

    I have used force values of 175, 200, and 250, with target-RMSD values of 0, 0.1 and 0.5 (in most combinations), and haven’t observed noticeable changes to the final RMSD. Nonetheless, the change in the speed of conformational change is apparent when I alter the force values, so I want to be cautious of using a “bad” force value. Is there a principled way of choosing the force value, so that the final structure is closer to the target structure? Or is the recommended value of 200 good enough even in the case that the structures have this much RMSD difference?

    Thank you very much for your time,

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