AMBER Archive (2005)

Subject: Re: AMBER: density profiles in ptraj or carnal

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon May 30 2005 - 12:00:08 CDT

> 1) I would like to see the graph of mass densities or electron
> densities of some solutes and solvent across the system box (distance).
> I searched ptraj or carnal for this analysis, but couldn't find that.
> How can I measure that by using ptraj or carnal?

Carnal doesn't do this, not sure about ptraj.

>
> 2) I know that I can measure moment of inertia by using carnal
> (groupid%momin). But, I'm wondering if I can do that in ptraj. How can
> I measure moment of inertia by using ptraj?
>
> 3) When I use ptraj, I know that I can specify analysis intervals by
> doing "trajin *** 100 200 1" (from 100ps to 200ps). But, how can I
> specify analysis intervals in CARNAL?

In carnal you could select the frames you want using OUTPUT COORD SELECT,
creating a new trajectory file, then analyze that.

However I suggest not using carnal as it will be discontinued.

Bill

>
> Thanks for your help in advance.
>
> best,
> Hwankyu.
>
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