[AMBER] Current rmsd from reference in targeted MD

From: Sonia Ziada <sonia.ziada.gmail.com>
Date: Tue, 3 Oct 2017 13:36:33 +0200

Dear Amber users,

I am having trouble understanding how the RMSD is calculated in targeted MD

I am using tgtfitmask (:Mask1) and tgtrmsmask (:Mask2).
I try to reproduce the sander output's targeted rmsd results (those
available in the mdout file: “current rmsd from reference”) using cpptraj
with the following commands:

### cpptraj script ---------------------------------
parm topo.top
trajin traj.nc
reference reference.rst
rms reference :Mask1
rms reference mass :Mask2 out rmsd.dat nofit

*But I get different results: *
### 1) From the .mdout file:
Current RMSD from reference: 0.017
Current RMSD from reference: 0.049
Current RMSD from reference: 0.075
Current RMSD from reference: 0.094
Current RMSD from reference: 0.110

### 2) From cpptraj (rmsd.dat file)
       1 0.0337
       2 0.0630
       3 0.0853
       4 0.1027
       5 0.1178

As far as I can conclude with these results, the TMD's alignment sceme
seems different from cpptraj's alignment sceme. How can I reproduce the
rmsd of the mdout using cpptraj ?
Thank you.

*ZIADA Sonia*
PhD Student, Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
d'Orléans 7311
Rue de Chartres, 45067 Orléans, France
T. +33 238 419 939
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Received on Tue Oct 03 2017 - 05:00:02 PDT
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