AMBER Archive (2005)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue May 31 2005 - 11:13:28 CDT

> How can I get three principal moments of inertia (Iz, Iy, Ix) ??

Modify the code.

> Before measuring them, do I need to reposition the solutes based on center of
> mass?

It might be appropriate to place the c.o.m. at the origin, but you'd
have to figure that out for yourself. I would do it in the
program automatically rather than rely on the user to do it.

Bill

>
> --------------------
> FILES_IN
> PARM p1 test.prmtop;
> STREAM s1 test.mdcrd;
> FILES_OUT
> TABLE t1 momin.tab;
> DECLARE
> GROUP grpid1 (RES 1,2,3,4,5,6,7,8,9);
> OUTPUT
> TABLE t1 grpid1%momin;
> END
> ---------------------
>
> best,
> Hwankyu.
>
>
> Quoting Bill Ross <ross_at_cgl.ucsf.edu>:
>
> >> 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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