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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Fri, 20 Jan 2017 16:54:29 -0500

On Wed, Jan 18, 2017 at 5:51 AM, Bala subramanian

<bala.biophysics.gmail.com> wrote:

*> Q1) From the rmsd matrix I calculated the AvgDist value of all the points
*

*> in cluster #0 and #1,and I get the values 3.749 (for #0) and 3.918 (#1).
*

*>
*

*> But cpptraj reports a value of 2.756 and 1.205 (see above). From the rmsd
*

*> matrix, it is easy to guess that the AvgDist is likely to be greater than
*

*> 2.7 and 1.2. Am I missing something in understanding cpptraj AvgDist ?.
*

AvgDist is the average of all point to point distances *within a

single cluster*. Make sure you're not double-counting (i.e. make sure

you're not using both distance of 1 to 2 and 2 to 1). Looking at the

RMSD matrix can be misleading since it contains distances between

points in different clusters as well.

*> Q2) Is there a way (in cpptraj) to dump the ascii pairdist file. I
*

Use the GitHub version of cpptraj

(https://github.com/Amber-MD/cpptraj) and you can read in cluster

matrices and treat them like a data set. So something like:

readdata PAIRD-BIN.dat name PW

writedata test.dat PW

should work.

*> converted the binary pairdist file to ascii format (using: hexdump -v -e
*

*> '10/4 "%06f "' -e '"\n"' PAIRD-BIN.dat > test.dat) and I get something like
*

*> pasted below. What do these trailing zeros mean ?
*

The binary format is well-described in the Amber 16 manual. Note also

in the GitHub version you can also write cluster matrices in netcdf

format (extension .nccmatrix), which may be easier to interact with

(although the matrix is still stored as a 1D array).

Hope this helps,

-Dan

*>
*

*> 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 3.333752
*

*> 1.000338 1.891641 4.172873 1.580285 7.259061 5.991429 7.105317 6.895642
*

*> 3.820035 3.972430 1.370469 3.610308 4.069707 2.705386 4.098798 3.704278
*

*> 0.992006 4.522664 1.088604 7.753875 6.499359 7.547778 7.335218 4.575821
*

*> 0.940676 7.760054 6.560380 7.492657 7.288205 4.467124 4.149098 2.685882
*

*> 4.407049 3.787850 7.268991 6.144238 6.942125 6.818217 1.503415 0.979665
*

*> 0.599390 1.988932 1.306563
*

*> 0.851417
*

*>
*

*> Thanks,
*

*> Bala
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> --
*

*> C. Balasubramanian
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

Date: Fri, 20 Jan 2017 16:54:29 -0500

On Wed, Jan 18, 2017 at 5:51 AM, Bala subramanian

<bala.biophysics.gmail.com> wrote:

AvgDist is the average of all point to point distances *within a

single cluster*. Make sure you're not double-counting (i.e. make sure

you're not using both distance of 1 to 2 and 2 to 1). Looking at the

RMSD matrix can be misleading since it contains distances between

points in different clusters as well.

Use the GitHub version of cpptraj

(https://github.com/Amber-MD/cpptraj) and you can read in cluster

matrices and treat them like a data set. So something like:

readdata PAIRD-BIN.dat name PW

writedata test.dat PW

should work.

The binary format is well-described in the Amber 16 manual. Note also

in the GitHub version you can also write cluster matrices in netcdf

format (extension .nccmatrix), which may be easier to interact with

(although the matrix is still stored as a 1D array).

Hope this helps,

-Dan

-- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jan 20 2017 - 14:00:02 PST

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