[obasekia]

Good day for the TMD simulation in the tutorial 9.1, how do we get the final_rmsd? do we get that by aligning both sate together and looking at the RMSD? i have a protein between two state if i align them together to get the RMSD my value is 5.744 which is higher than the reference value of 4.3. how should i go about it? Secondly can i use implicit model for the TMD?

[ckobayashi]

Hello,

The TMD (SMD) method brings a structure closer to the TARGET structure (=reffile in [INPUT]) . Then,  the ‘final_rmsd’ values should be a small value (< 1.0 Angstrom). If not, that is, if the RMSD is somewhat large, there is no certainty that two structures with the same RMSD value are close structures.

I am not sure if I am answering your question properly because I cannot catch your question.

As for the second question, it should be possible.

 

Kobayashi

 

[obasekia]

How do you determine the final_rmsd AND is the reference value in the tutorial always 4.3 irrespective of the protein?

[ckobayashi]

We made ‘final_rmsd’ small enough to be close to the target structure. However, due to thermal motion, it is not set to zero to prevent very strong external forces from being applied to the system.

As for the reference values (reference1), rmsd of the initial structure from the targeted structure is calculated.  The value  will be different depending on the protein and initial structure.

(I also note that the reference is updated during the simulation. )

[obasekia]

Thanks for the explanation