as you can tell from the rmsd value of 0, the first rmsd calculation is
done on your inpcrd.
On Wed, Oct 4, 2017 at 8:25 AM, Sonia Ziada <sonia.ziada.gmail.com> wrote:
> Ok I did it and the result is surprising :
>
> ### 1) From the .mdout file:
> Current RMSD from reference: 0.000
> Current RMSD from reference: 0.017
> Current RMSD from reference: 0.034
> Current RMSD from reference: 0.049
> Current RMSD from reference: 0.063
> Current RMSD from reference: 0.075
> Current RMSD from reference: 0.085
> Current RMSD from reference: 0.094
> Current RMSD from reference: 0.103
> Current RMSD from reference: 0.110
>
> ### 2) From cpptraj (rmsd.dat file)
> #Frame RMSD_00002
> 1 0.0172
> 2 0.0337
> 3 0.0491
> 4 0.0630
> 5 0.0752
> 6 0.0853
> 7 0.0942
> 8 0.1027
> 9 0.1106
> 10 0.1178
>
> Does it mean that the first frame in the trajectory does not correspond to
> the first step of the simulation but rather the second OR that the first
> block in the mdout (NSTEP=1) does not correspond to the first step of the
> simulation but rather to the step 0, that is the restart ?
>
> 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
>
> 2017-10-04 12:30 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com
> >:
>
> > Can you try writing structures every step?
> >
> > On Oct 3, 2017 5:05 PM, "Sonia Ziada" <sonia.ziada.gmail.com> wrote:
> >
> > > 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
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Received on Wed Oct 04 2017 - 06:00:05 PDT
