- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Sylvester Tumusiime <stumusii.uno.edu>

Date: Fri, 22 May 2015 19:48:26 +0000

Dear Amber user,

I came across this advice on the amber mailing list concerning the use of

xmgrace to determine number of water molecules from a point:

"It sounds to me like the analysis you want to do is to calculate a radial

distribution function in ptraj (which will effectively give you a graph of

how many solvent molecules are present as a function of distance from a

given solute mask). This is described in the manual via the "radial"

command.

If you integrate the RDF from 0 to whichever distance you want, that should

give you the number of water molecules within that distance cutoff of the

Zn ion (something that xmgrace does very easily under

Data->Transformations->Integration)".

My question is asked to clarify on the point made in the advice. From my

understanding, the value given after following: Data -> Transformations ->

Integration is the total number of water molecules (i.e. the area under the

entire curve from 0 to the last point on the x-axis). Am i correct in

assuming that? I have performed a test where i have a smaller value on the

x-axis as the end point and it seems to agree with this assumption. Am only

asking so as to make sure that my assumption is not wrong.

Thank you

Syl

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Fri May 22 2015 - 13:00:04 PDT

Date: Fri, 22 May 2015 19:48:26 +0000

Dear Amber user,

I came across this advice on the amber mailing list concerning the use of

xmgrace to determine number of water molecules from a point:

"It sounds to me like the analysis you want to do is to calculate a radial

distribution function in ptraj (which will effectively give you a graph of

how many solvent molecules are present as a function of distance from a

given solute mask). This is described in the manual via the "radial"

command.

If you integrate the RDF from 0 to whichever distance you want, that should

give you the number of water molecules within that distance cutoff of the

Zn ion (something that xmgrace does very easily under

Data->Transformations->Integration)".

My question is asked to clarify on the point made in the advice. From my

understanding, the value given after following: Data -> Transformations ->

Integration is the total number of water molecules (i.e. the area under the

entire curve from 0 to the last point on the x-axis). Am i correct in

assuming that? I have performed a test where i have a smaller value on the

x-axis as the end point and it seems to agree with this assumption. Am only

asking so as to make sure that my assumption is not wrong.

Thank you

Syl

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Fri May 22 2015 - 13:00:04 PDT

Custom Search