Re: [AMBER] NFE, PMD, and MULTI_RMSD questions

From: Feng Pan <>
Date: Wed, 14 Mar 2018 14:31:32 -0400

Hi, Russell

Yes, the cv_r gives the reference coordinates for calculating RMSD.
As your description in your case, the initial value should be 17 Ang if you
the crystal structure as the reference. I would recommend you to double
that the atom index and coordinates are correct in the CV input file. Also
you can
send me your input files and I can check for you.


On Tue, Mar 13, 2018 at 7:26 PM, Russell Davidson <> wrote:

> Dear all,
> I am currently attempting to run a set of 1D umbrella sampling simulations
> using the NFE method, specifically the pinned MD namelist, to obtain the
> relative free energies of various conformations of a loop region in a
> protein. This loop region is highly mobile during unbiased simulations,
> having RMSD values that range up to ~17 Ang relative to the crystal
> structure. The protocol used for this RMSD analysis uses an alignment
> landmark (C_alpha atoms of protein residues that have low mobility over the
> course of the trajectory) to align the analysis frame to the reference
> frame, subsequently followed by a RMSD calculation of the loop region.
> To enhance sampling of the conformations of the loop region, I would like
> to use the MULTI_RMSD reaction coordinate but am running into unexpected
> results. I start a US window from a frame with a 17 Ang RMSD value with the
> harmonic biasing potential centered at 17 Ang. Additionally, I am applying
> a restraint (using ntr=1 in the &cntrl namelist) to the alignment landmark,
> thereby preventing COM translation and rotation of my protein away from the
> reference structure (crystal structure). With this simulation setup, the
> collective variable output file is reporting RMSD values of ~2 Ang. I
> hypothesize that the MULTI_RMSD colvar aligns the biased atom selection to
> the reference cartesian coordinates (defined in the cv_r variable) before
> calculating the RMSD. Is this true? Can anyone point me to the code that is
> used to calculate the RMSD values? Any further insight into the MULTI_RMSD
> colvar would be greatly appreciated.
> Thanks!
> Russell Davidson
> _______________________________________________
> AMBER mailing list

Feng Pan
North Carolina State University
Department of Physics
AMBER mailing list
Received on Wed Mar 14 2018 - 12:00:03 PDT
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