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#36083 - 12/15/16 02:04 PM Vibran module of Charmm
fara Offline
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Registered: 12/14/16
Posts: 8
Hi everyone!

I have some questions about Vibran module of Charmm.
Is Vibran an all atomic normal mode analysis?
Is it analytical or numerical?
Is it just in the basis of Charmm Forcefields?
Can this module obtain and report the eigenvectors or just can report the amount of frequencies?

Thank you in advance!
Fara

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#36084 - 12/15/16 03:23 PM Re: Vibran module of Charmm [Re: fara]
lennart Online   content

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Loc: ~ 59N, 15E
Is Vibran an all atomic normal mode analysis?
*** Yes (it uses the force field you read), but there are also ways of coarse-graining the NMA.
Is it analytical or numerical?
*** Analytical
Is it just in the basis of Charmm Forcefields?
*** No, any force field can be used, and there are also ways of coarse-graining the NMA.
Can this module obtain and report the eigenvectors or just can report the amount of frequencies?
*** Eigenvectors are available and can be reported.

Please read vibran.doc and formulate more precise questions.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#36424 - 06/06/17 03:09 PM Re: Vibran module of Charmm [Re: lennart]
fara Offline
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Registered: 12/14/16
Posts: 8
Dear Lennart,
Thank you very much for your answers.

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#36425 - 06/06/17 03:33 PM Re: Vibran module of Charmm [Re: lennart]
fara Offline
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Registered: 12/14/16
Posts: 8
Dear Lennart,

Thanks again for your response!

Do you know any sample documemt as an example to use vibran mode of charmm?

Best Regards,
Fara



Edited by fara (06/06/17 03:33 PM)

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#36426 - 06/07/17 01:44 AM Re: Vibran module of Charmm [Re: fara]
lennart Online   content

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Registered: 09/25/03
Posts: 4622
Loc: ~ 59N, 15E
I assume that your system is small.

After reading RTF, paramaters, PSF (or generating the PSF), and coordinates for your small molecule:

minimize abnr nstep 5000 cutnb 14.0 ctofnb 12.0 ctonnb 10.0 vswitch fshift
calc nm = 3 * ?natom
vibran nmodes @nm
diag nfreq @nm
end
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#36427 - 06/08/17 12:37 PM Re: Vibran module of Charmm [Re: lennart]
fara Offline
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Registered: 12/14/16
Posts: 8
Dear Lennart,

Thank you very much for your help!

My system is about 500 atoms. Is there any atom number limitation? I should mention that I would like to use all atomic normal mode analysis for my work.

Best Regards,
Fara

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#36430 - 06/08/17 01:58 PM Re: Vibran module of Charmm [Re: fara]
rmv Online   content

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Posts: 8097
Loc: 39 03 48 N, 77 06 54 W
The soft limit of 300 atoms may still be in place, so you may need to set BOMLEV -2 prior to starting VIBRAN.
_________________________
Rick Venable
computational chemist


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#36431 - 06/09/17 11:40 AM Re: Vibran module of Charmm [Re: rmv]
fara Offline
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Registered: 12/14/16
Posts: 8
Dear Rick,

Thank you for your guidance!

Best Regards,
Fara


Edited by fara (06/09/17 12:15 PM)

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#36480 - 07/07/17 06:22 PM Re: Vibran module of Charmm [Re: fara]
fara Offline
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Registered: 12/14/16
Posts: 8
Hi

I have another question about the VIBRAN module of Charmm. Has VIBRAN included the cross-term (CMAP) in the normal mode analysis calculation?

Best Regards,
Fara


Edited by fara (07/07/17 06:24 PM)

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#36481 - 07/08/17 12:33 PM Re: Vibran module of Charmm [Re: fara]
rmv Online   content

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Registered: 09/17/03
Posts: 8097
Loc: 39 03 48 N, 77 06 54 W
Not sure, but you should be able to test that easily by doing normal modes with CMAP disabled via

SKIPE CMAP

prior to starting VIBRAN


_________________________
Rick Venable
computational chemist


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