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From: <kartik.lakshmi.gmail.com>

Date: Mon, 29 Jun 2020 18:22:56 -0700

Hi Daniel!

Thanks for the help. I agree I need more sampling to converge the RMSFs from

these two independent runs.

-Kartik

Sent from [1]Mail for Windows 10

From: [2]Daniel Roe

Sent: 29 June 2020 17:59

To: [3]AMBER Mailing List

Subject: Re: [AMBER] Problems with RMSF calculations

Hi,

On Mon, Jun 29, 2020 at 4:47 PM <kartik.lakshmi.gmail.com> wrote:

* >
*

* > However, when I replace this formula and compute deviations wrt a
*

reference

* > value (see Case II), I do get RMSF34 > RMSF1234 > RMSF12. Since I do
*

supply

* > a reference frame (first frame) I would have expected cpptraj to be
*

doing

* > something like Case II.
*

The reference gets used by the rms command (thereby best-fitting on

the specified reference and removing global rotation/translation) but

reference structures are *not* used by atomicfluct (nowhere in the

manual entry is it said reference structures are employed). Going back

to the original question, there are two independent MD trajectories

starting from the same initial coordinates. The fact that the RMSF

profile of the first trajectory is different from the second

trajectory simply indicates that the atoms are undergoing somewhat

different motions in each simulation, ergo the two trajectories are

not converged. This is a perfectly reasonable result with limited

sampling.

-Dan

* >
*

* >
*

* > If indeed the formula being used is similar to the Case I formula then
*

what

* > is the use of the reference. Using the average position as reference
*

(as

* > Kenneth suggested earlier) seems redundant.
*

* >
*

* >
*

* > Thanks a lot for all the help!
*

* >
*

* > Kartik
*

* >
*

* >
*

* >
*

* >
*

* >
*

* > From: [1]Daniel Roe
*

* > Sent: 29 June 2020 09:02
*

* > To: [2]AMBER Mailing List
*

* > Subject: Re: [AMBER] Problems with RMSF calculations
*

* >
*

* >
*

* > Hi,
*

* >
*

* >
*

* > On Fri, Jun 26, 2020 at 2:49 PM <kartik.lakshmi.gmail.com> wrote:
*

* >
*

* > > I would expect the RMSF calculated using this script to give the
*

* > average
*

* >
*

* > > RMSF from the two production runs
*

* >
*

* >
*

* > This isn't correct, and the short explanation is because the RMSF
*

* >
*

* > calculation involves a square root. You can convince yourself of this
*

* >
*

* > by taking a simple set of numbers (like 4 5 3 4) and plug them into
*

* >
*

* > the RMSF formula ( RMSF1234 = sqrt(AvgSumSq - Avg^2), where AvgSumSq
*

* >
*

* > is the average of the sum of squares of the values and Avg is the
*

* >
*

* > average of the values. Then calculate RMSF for the first two and last
*

* >
*

* > two values (call them RMSF12 and RMSF34). You'll see that the average
*

* >
*

* > of RMSF12 and RMSF34 is not RMSF1234. Hope this helps,
*

* >
*

* >
*

* > -Dan
*

* >
*

* >
*

* > > 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
*

* >
*

* >
*

* > _______________________________________________
*

* >
*

* > AMBER mailing list
*

* >
*

* > AMBER.ambermd.org
*

* >
*

* > http://lists.ambermd.org/mailman/listinfo/amber
*

* >
*

* > References
*

* >
*

* > 1. mailto:daniel.r.roe.gmail.com
*

* > 2. mailto:amber.ambermd.org
*

* > _______________________________________________
*

* > 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

References

1. https://go.microsoft.com/fwlink/?LinkId=550986

2. mailto:daniel.r.roe.gmail.com

3. mailto:amber.ambermd.org

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jun 29 2020 - 18:30:03 PDT

Date: Mon, 29 Jun 2020 18:22:56 -0700

Hi Daniel!

Thanks for the help. I agree I need more sampling to converge the RMSFs from

these two independent runs.

-Kartik

Sent from [1]Mail for Windows 10

From: [2]Daniel Roe

Sent: 29 June 2020 17:59

To: [3]AMBER Mailing List

Subject: Re: [AMBER] Problems with RMSF calculations

Hi,

On Mon, Jun 29, 2020 at 4:47 PM <kartik.lakshmi.gmail.com> wrote:

reference

supply

doing

The reference gets used by the rms command (thereby best-fitting on

the specified reference and removing global rotation/translation) but

reference structures are *not* used by atomicfluct (nowhere in the

manual entry is it said reference structures are employed). Going back

to the original question, there are two independent MD trajectories

starting from the same initial coordinates. The fact that the RMSF

profile of the first trajectory is different from the second

trajectory simply indicates that the atoms are undergoing somewhat

different motions in each simulation, ergo the two trajectories are

not converged. This is a perfectly reasonable result with limited

sampling.

-Dan

what

(as

trajectories.

entire

(for

using

(i.e.

https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8

https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8

https://urldefense.com/v3/__http:/wt_pd.nc__;!!Mih3wA!RkWVHZ9uzYaTsfRwSkKOl8

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

References

1. https://go.microsoft.com/fwlink/?LinkId=550986

2. mailto:daniel.r.roe.gmail.com

3. mailto:amber.ambermd.org

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jun 29 2020 - 18:30:03 PDT

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