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From: David A. Case <case.scripps.edu>

Date: Thu, 6 May 2004 08:29:30 -0700

On Thu, May 06, 2004, Marcin Krol wrote:

*> I have tried to calculate mass weighted covariance matrix and analyze it,
*

*> obtaining entropy contributions. the ptraj script that does it is very
*

*> simple:
*

*>
*

*> trajin traje.file (I have oriented all frames on the starting structure)
*

*> matrix mwcowar name mwc200 out mwc200.dat start 1 stop 201
*

*> analyze matrix mwc200 out mwc200_ana.dat thermo vecs 0
*

*>
*

*> However, if the number 3*N (N-atoms) is larger than 200 I get starnge
*

*> results:
*

*> 1. I get a warning: setting vibrational entropy to zero for mode 201 with
*

*> vtemp = -319766250.735258
*

If you have only 200 snapshots, then the maximum number of quasiharmonic

modes you can obtain is 200 (independent of the number of atoms). This is

because the linear space spanned by your snapshots can be completely described

with 200 vectors, and no other ones make sense.

The program should give a better message in this case, but you can ignore

the results for modes that are greater than the number of snapshots.

However, you should also know that with so few snapshots, you will almost

certainly not get a converged estimate of the conformational entropy.

[Holger: we (you?) should probably adjust the code to recognize than all

modes above the number of snapshots used is irrelevant. But I'm not sure

how easy this will be, since the "analyze matrix" command may not necessarily

know how the matrix was constucted.]

....good luck...dac

Date: Thu, 6 May 2004 08:29:30 -0700

On Thu, May 06, 2004, Marcin Krol wrote:

If you have only 200 snapshots, then the maximum number of quasiharmonic

modes you can obtain is 200 (independent of the number of atoms). This is

because the linear space spanned by your snapshots can be completely described

with 200 vectors, and no other ones make sense.

The program should give a better message in this case, but you can ignore

the results for modes that are greater than the number of snapshots.

However, you should also know that with so few snapshots, you will almost

certainly not get a converged estimate of the conformational entropy.

[Holger: we (you?) should probably adjust the code to recognize than all

modes above the number of snapshots used is irrelevant. But I'm not sure

how easy this will be, since the "analyze matrix" command may not necessarily

know how the matrix was constucted.]

....good luck...dac

-- ================================================================== David A. Case | e-mail: case.scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Thu May 06 2004 - 16:53:00 PDT

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