are you certain that the structures that you are using in ptraj correspond
exactly to those in the MD run? for example, are you writing every step?
and are you using netcdf format instead of the low precision trajectory
files?
On Tue, Oct 3, 2017 at 7:36 AM, Sonia Ziada <sonia.ziada.gmail.com> wrote:
> Dear Amber users,
>
> I am having trouble understanding how the RMSD is calculated in targeted MD
> simulations.
>
> 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
> run
> quit
> --------------------------------------------------------
>
>
> *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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Oct 03 2017 - 10:00:03 PDT
