ERMSD

[gsabbih6]

How will I use ERMSD collective variables?

[giacomofiorin]

Hi Godfred, I presume you mean this type of CV that is provided by PLUMED: https://www.plumed.org/doc-v2.8/user-doc/html/_e_r_m_s_d.html https://doi.org/10.1093/nar/gku972

At the moment, Colvars doesn't provide such a function. Are you trying to model a nucleic acid structure specifically or do you have a different problem for which we could suggest alternatives? Which MD engine and computational hardware platform are you using?

[gsabbih6]

Hi Giacomo,

Yes I am trying to model a nucleic acid using NAMD on Linux clusters (Huge resources).

Yeah, I read ERMSD is good for RNA dynamics. What would you suggest in this case

thanks

[giacomofiorin]

From the look of it it is a good general CV to treat conformational changes in RNA. I have no reason to question the statement that straight RMSD is inaccurate for RNA, I'm not sure I can suggest quickly anything better for general use. I think rebuilding NAMD with Plumed is worth considering.

If you have a good idea of the conformational change that you're expecting for your specific problem, you can try one of the other available functions in Colvars, optionally customized further with a scripted or custom function. That does not require developing new C++ code.

[giacomofiorin]

@gsabbih6 Did you find out how you want to proceed next? Is there anything that can be done within this discussion?

[gsabbih6]

I tried others CVs and also patched Namd with PLUMED. Thanks

Godfred

On Fri, Sep 9, 2022, 4:20 PM Giacomo Fiorin @.***> wrote:

@gsabbih6 https://github.com/gsabbih6 Did you find out how you want to proceed next? Is there anything that can be done within this discussion?

— Reply to this email directly, view it on GitHub https://github.com/Colvars/colvars/issues/495#issuecomment-1242422825, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACGW45A5RQ5DXAISQHZOFCDV5OLYFANCNFSM6AAAAAAQC7GBZU . You are receiving this because you were mentioned.Message ID: @.***>