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From: kepa koldo burusco <kepaquestions.yahoo.es>

Date: Thu, 15 Mar 2007 12:46:17 +0100 (CET)

[15-III-2007]

Hello Amber users,

I have 2 small doubts and maybe someone could help me

a little...

I have run a MD calculations for a set of molecules in

vacuum. Now I would like to calculate the dipolar

moment and also the inertia moments from the

trajectory.

I succesfully did it with ptraj (amber 7 version, the

one we use here), but the output files are a bit weird

for me (especially the ones for the inertia axis...).

The output format for both calculations are, as you

probably know, 10 columns: first one is the snapshot

number, the next 3 ones are the XYZ coordinates for

the vector, the next 3 ones are the XYZ coordinates

for the center of mass, and the last 3 ones are the

XYZ coordinates of the vector framed into the center

of mass system of coordinates.

That seems to be OK for the dipolar moment (I am only

interested in the module of the vector). But I don't

really understand what's going on with the inertia

moments. I mean, I am getting 3 output files (one for

each coordinate X, Y and Z) having also 10 columns...

I mean, I am interested in getting the 3 Moments of

Inertia (for calculating esphericity) but I think that

ptraj is calculating the 3 eigenvectors instead...

Am i right? Does anyone know whether it is possible to

get the 3 eigenvalues using ptraj? If yes... which

version of ptraj?

I'm attaching the input file for ptraj and the 3

output files just to make it clearer for you.

Thank you very much in advance!!!

Kepa K. Burusco

**********************************

PhD Student

Universidad Autonoma de Barcelona

**********************************

______________________________________________

LLama Gratis a cualquier PC del Mundo.

Llamadas a fijos y móviles desde 1 céntimo por minuto.

http://es.voice.yahoo.com

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Received on Sun Mar 18 2007 - 06:07:20 PDT

Date: Thu, 15 Mar 2007 12:46:17 +0100 (CET)

[15-III-2007]

Hello Amber users,

I have 2 small doubts and maybe someone could help me

a little...

I have run a MD calculations for a set of molecules in

vacuum. Now I would like to calculate the dipolar

moment and also the inertia moments from the

trajectory.

I succesfully did it with ptraj (amber 7 version, the

one we use here), but the output files are a bit weird

for me (especially the ones for the inertia axis...).

The output format for both calculations are, as you

probably know, 10 columns: first one is the snapshot

number, the next 3 ones are the XYZ coordinates for

the vector, the next 3 ones are the XYZ coordinates

for the center of mass, and the last 3 ones are the

XYZ coordinates of the vector framed into the center

of mass system of coordinates.

That seems to be OK for the dipolar moment (I am only

interested in the module of the vector). But I don't

really understand what's going on with the inertia

moments. I mean, I am getting 3 output files (one for

each coordinate X, Y and Z) having also 10 columns...

I mean, I am interested in getting the 3 Moments of

Inertia (for calculating esphericity) but I think that

ptraj is calculating the 3 eigenvectors instead...

Am i right? Does anyone know whether it is possible to

get the 3 eigenvalues using ptraj? If yes... which

version of ptraj?

I'm attaching the input file for ptraj and the 3

output files just to make it clearer for you.

Thank you very much in advance!!!

Kepa K. Burusco

**********************************

PhD Student

Universidad Autonoma de Barcelona

**********************************

______________________________________________

LLama Gratis a cualquier PC del Mundo.

Llamadas a fijos y móviles desde 1 céntimo por minuto.

http://es.voice.yahoo.com

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

- application/octet-stream attachment: 3508478787-inertia.trajin

- application/octet-stream attachment: 424567105-GLI_lin_stp2.inx

- application/octet-stream attachment: 285303791-GLI_lin_stp2.iny

- application/octet-stream attachment: 3014350063-GLI_lin_stp2.inz

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