Dear Carlos,
Thank you for your reply.
- I am writing the trajectory (netcdf file) and the mdout every 2 steps
(ntwx=2 and ntpr=2), so the structures used in cpptraj should correspond
exactly to those in the MD run.
- I am sure that the reference used for the fitting in the MD run is the
same that those I use in cpptraj
- I have also checked that the masks are correct (by looking at: the header
of the mdout, the output of cpptraj and by using ambmask program)
- Finally, I have a looked at the ene.F90 sander script containing the
subroutine fitrms (that calcutes the current rmsd after the fitting step)
to ensure that the rmsd is mass weighted.
I do not understand the difference in rmsd values between cpptraj and the
mdout file. By calcutating the rmsd with cpptraj, I assumed that the
alignment algorithm is the same in cpptraj as in sander. But is this true?
*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
2017-10-03 18:44 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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 - 14:30:02 PDT
