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#36590 - 09/16/17 05:22 AM Generate sparse Hessian matrix?
Hyuntae Offline
Forum Member

Registered: 05/09/12
Posts: 3
I want to get sparse Hessian matrix of very large system, in binary or text format (with keeping large number of digits). Is there any way to generate the sparse Hessian matrix?

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#36603 - 09/24/17 09:55 PM Re: Generate sparse Hessian matrix? [Re: Hyuntae]
Hyuntae Offline
Forum Member

Registered: 05/09/12
Posts: 3
To CHARMM experts,

I could get Hessian matrix entities using the following commands:

! read topology and parameter file
read rtf card name top.rtf
read param card name par.prm
! read the psf and coordinate file
read psf card name target.psf
read coor card name target.crd
BOMLEV -5
vibran elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10. VSWITCH SWITCH CDIE
open unit 1 write form name "second2.dat"
write second card unit 1
close unit 1


I want to get sparse Hessian matrix, which contains only non-zero elements.

From documents at:
https://www.charmm.org/charmm/documentation/by-version/c42b1/params/doc/vibran/

I could find about "REDU CMPAct" option. I tried several things, but I could not figure out how to generate the sparse Hessian matrix...

I hope to get any help.

Thank you in advance.

Best regards,
-- Hyuntae

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