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From: erik zuiderweg <erikzuiderweg.gmail.com>

Date: Tue, 7 Jan 2020 18:08:28 +0100

I am using Amber16, and try to compute N-H P2 correlation functions from a protein MD run, to compare with NMR relaxation data.

this is my CPPTRAJ script

cpptraj ../BETA_APO.top << EOF

trajin ../BETA_APO_MIN_HEAT_EQUIL_MD.x 1 800

vector v2 :2.H :2.N

analyze timecorr vec1 v2 out corr_2_NH

EOF

The output file corr_2_NH contains 800 entries.

I find this strange — how can one get a correlation between entries that are 800 part from just 800 files? — the last one is an average of 1!

I guess I should just trust the first quarter or so?

Second question concerns the entire concept of P2 correlation functions fom MD trajectories.

In real life, the P2 is taken between the direction of the NH vector and the magnetic field.

So one approach could be to take the PDB Z-direction as the reference vector.

But why not X, or. Y?

And, a wiggle in the XY plane does not change the angle with Z.

In real life of course, all this does not matter so much — for most proteins the molecular frame tumbles more or less isotropicaly so all reference directions become more or less equivalent.

But with an MD ensemble that is rotationally static, the “magnetic field “ axis choice should matter.

I figure a good reference vector for the P2 calculation may be the average direction of the N-H vector. Than one should not miss any wiggles in any direction.

Thus programming that in ancient Fortran, I find normalized NH correlation functions for residue 2 which comes down to an “order parameter plateau” of 0.95 or so, while the ptraj goes down to 0.7 …

Now I could very well make a mistake in programming, but I wonder how these reference axis issues are dealt with in CPPTRAJ?

Erik R.P. Zuiderweg

Professor Emeritus

Department of Biological Chemistry

University of Michigan Medical School

Ann Arbor, MI, USA

Guest Professor, Institute for Molecules and Materials,

Radboud University, Nijmegen,

The Netherlands

zuiderwe.umich.edu

(+31) 611154835

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Tue Jan 07 2020 - 09:30:03 PST

Date: Tue, 7 Jan 2020 18:08:28 +0100

I am using Amber16, and try to compute N-H P2 correlation functions from a protein MD run, to compare with NMR relaxation data.

this is my CPPTRAJ script

cpptraj ../BETA_APO.top << EOF

trajin ../BETA_APO_MIN_HEAT_EQUIL_MD.x 1 800

vector v2 :2.H :2.N

analyze timecorr vec1 v2 out corr_2_NH

EOF

The output file corr_2_NH contains 800 entries.

I find this strange — how can one get a correlation between entries that are 800 part from just 800 files? — the last one is an average of 1!

I guess I should just trust the first quarter or so?

Second question concerns the entire concept of P2 correlation functions fom MD trajectories.

In real life, the P2 is taken between the direction of the NH vector and the magnetic field.

So one approach could be to take the PDB Z-direction as the reference vector.

But why not X, or. Y?

And, a wiggle in the XY plane does not change the angle with Z.

In real life of course, all this does not matter so much — for most proteins the molecular frame tumbles more or less isotropicaly so all reference directions become more or less equivalent.

But with an MD ensemble that is rotationally static, the “magnetic field “ axis choice should matter.

I figure a good reference vector for the P2 calculation may be the average direction of the N-H vector. Than one should not miss any wiggles in any direction.

Thus programming that in ancient Fortran, I find normalized NH correlation functions for residue 2 which comes down to an “order parameter plateau” of 0.95 or so, while the ptraj goes down to 0.7 …

Now I could very well make a mistake in programming, but I wonder how these reference axis issues are dealt with in CPPTRAJ?

Erik R.P. Zuiderweg

Professor Emeritus

Department of Biological Chemistry

University of Michigan Medical School

Ann Arbor, MI, USA

Guest Professor, Institute for Molecules and Materials,

Radboud University, Nijmegen,

The Netherlands

zuiderwe.umich.edu

(+31) 611154835

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Tue Jan 07 2020 - 09:30:03 PST

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