Ok. Now I understood how it works.
Thank you very much.
*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 15:04 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> you can't generate forces for the first step of MD without doing the
> overlap calculation, so it will be done regardless of ntwx or ntpr.
>
> On Wed, Oct 4, 2017 at 8:45 AM, Sonia Ziada <sonia.ziada.gmail.com> wrote:
>
> > Or it can be that the change is so small after 1 step simulation that the
> > rmsd is still equal to 0.
> > Because if the first rmsd calculation is done on the inpcrd, the first
> > value should be equal to zero even for ntwx=2 and ntpr=2 simulation. Or
> am
> > I wrong ?
> >
> > *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 14:38 GMT+02:00 Carlos Simmerling <
> carlos.simmerling.gmail.com
> > >:
> >
> > > 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
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 04 2017 - 08:30:02 PDT
