Date: Sat, 27 Jun 2020 12:56:05 -0700
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/
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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References
1. mailto:kennethneltharion.gmail.com
2. mailto:amber.ambermd.org
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(image/png attachment: RMSF.PNG)
