Hi,
I don’t think cpptraj RMSF script is
> actually giving me the anticipated ‘average’ value of the RMSF when
> using
> two 250 ns simulations.
>
So the thing that jumps to mind- when you RMS the individual 250 portions,
I'm guessing it goes something like
parm *.prmtop
trajin prod1.nc 1 last 1
rms .CA first
rmsf .CA out rmsf_1.dat
parm *.prmtop
trajin prod2.nc 1 last 1
rms .CA first
rmsf .CA out rmsf_1.dat
So the trick is that the point of reference you RMS to for each portion
varies, ie the first frame of that 250 ns portion is going to vary between
the two unless you've specifically load up the same frame to work as a
reference. So to keep a 'consistent' comparison it might be something more
like
parm *.prmtop
trajin first_ref.pdb 1 1 1
trajin prod2.nc 1 last 1
rms @CA first
rmsf .CA out rmsf_1.dat
That said, taking an average of two averages is a little tricky, especially
if they're subsections of the same time series.
Best,
Kenneth
On Sat, Jun 27, 2020 at 3:56 PM <kartik.lakshmi.gmail.com> wrote:
>
> Hi Kenneth,
>
>
> Thanks for your suggestion! I tried to use the rms @CA first out
> rms.out to
> ensure that I am using the first frame as a reference and my results
> look
> exactly as the one from the older version of the cpptraj script (with
> reference ../../prod/pd1/wt_pd.nc 1 statement ). The attached graph
> can show
> that it is identical to the one I send earlier.
>
>
> Hence my problem still remains. I don’t think cpptraj RMSF script is
> actually giving me the anticipated ‘average’ value of the RMSF when
> using
> two 250 ns simulations.
>
>
> I would appreciate any suggestions and explanations!
>
>
> Thanks a lot in advance,
>
> Kartik
>
>
>
> From: [1]Kenneth Huang
> Sent: 26 June 2020 14:50
> To: [2]AMBER Mailing List
> Subject: Re: [AMBER] Problems with RMSF calculations
>
>
> Hi,
>
>
> My guess is the it might not be fitting to to the first frame- you can
> try
>
>
> parm ../../prod/pd1/wt.prmtop
>
> trajin ../../prod/pd1/[1]wt_[2]pd.nc
>
> trajin ../../prod/pd2/[3]wt_[4]pd.nc
>
> rms .CA first out rms.out
>
> atomicfluct out RMSF.dat @CA byres
>
>
> Which should avoid any ambiguity of if it's fetching the wrong frame.
>
>
> Best,
>
>
> Kenneth
>
>
> On Fri, Jun 26, 2020 at 2:49 PM <kartik.lakshmi.gmail.com> wrote:
>
>
> >
>
> >
>
> > I have a total of 500 ns trajectory - 250 + 250 ns - starting from
> the
>
> > same
>
> > eq.rst file. I calculated the RMSF (wrt to the first frame as the
>
> > reference)
>
> > for this 500 ns using this cpptraj script:
>
> >
>
> > parm ../../prod/pd1/wt.prmtop
>
> > trajin ../../prod/pd1/[1]wt_[2]pd.nc
>
> > trajin ../../prod/pd2/[3]wt_[4]pd.nc
>
> > reference ../../prod/pd1/[5]wt_[6]pd.nc 1
>
> > rms .CA reference
>
> > atomicfluct out RMSF.dat @CA byres
>
> > run
>
> >
>
> >
>
> > I would expect the RMSF calculated using this script to give the
> average
>
> > RMSF from the two production runs but it seems that the RMSF
> calculated
>
> > using the input above is not the true average of the two
> trajectories.
>
> >
>
> >
>
> > The attached graph will make it clearer.
>
> > comp_mean.png contains the RMSF calculated using cpptraj for the
> entire
>
> > PD1
>
> > and PD2 and for PD1 + PD2. I have also plotted here the mean RMSFs
> (for
>
> > 10ns
>
> > chunks) for PD 1 and PD 2 that I calculated using python. Am I
> using
> the
>
> > RMSF script incorrectly? I want to calculate the residue-wise
>
> > fluctuations
>
> > of the Ca atoms of the peptide backbone of my entire simulation
> (i.e.
>
> > PD 1
>
> > and 2 combined).
>
> >
>
> >
>
> > Thanks a lot in advance for all the help!
>
> >
>
> > Kartik Lakshmi Rallapalli
>
> >
>
> > References
>
> >
>
> > 1.
>
> >
>
> https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8
> GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
>
> > 2. http://pd.nc/
>
> > 3.
>
> >
>
> https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8
> GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
>
> > 4. http://pd.nc/
>
> > 5.
>
> >
>
> https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8
> GwVSF_aGB56sRRlI2gEzyf_i_Lj7VJPgwZCZ9m$
>
> > 6. http://pd.nc/
>
> > _______________________________________________
>
> > AMBER mailing list
>
> > AMBER.ambermd.org
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
>
>
> --
>
> Ask yourselves, all of you, what power would hell have if those
> imprisoned
>
> here could not dream of heaven?
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> References
>
> 1. mailto:kennethneltharion.gmail.com
> 2. mailto:amber.ambermd.org
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Sat Jun 27 2020 - 16:00:04 PDT
