Re: [AMBER] Problem of Steered MD Simulation for unfolding of RNA

From: Leena Aggarwal <>
Date: Thu, 2 Jul 2020 20:13:04 +0530

As per my knowledge, I think you need to prepare a collective variable file
i.e cv_file used for smd simulations in which the reaction coordinate can
be considered as MULTI_RMSD (cv_type). Next mention the group of atoms of
RNA which you want to pull in cv_i and mention the reference position of
atoms in the cv_r list. You also need to mention the harmonic constant for
the run. Define the &smd namelist (this refers to the cv_file) below
&cntrl namelist in mdin file.
SMD applies the force according to the harmonic constant on the group of
atoms of RNA that you want to pull and gives the change in the coordinates
in the form of RMSD within a certain time in the output file mentioned
below &smd namelist.

On Thu, Jul 2, 2020, 17:16 Vishal Singh <> wrote:

> Dear AMBER Users
> I want to perform Steered Molecular Dynamics (SMD) Simulation for the
> unfolding of RNA. But I did not find any suitable listed tutorial for this.
> How can I input the spring constant and the pulling velocity values in SMD
> simulation for the calculation of a force-extension curve for the unfolding
> of RNA ?
> Thanks.
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Received on Thu Jul 02 2020 - 08:00:03 PDT
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