ni <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Tuesday, July 17, 2007 1:30:22 AM
Subject: Re: [gmx-users] which tool to use a measure a user-defined angle in a
traj
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it out (b/c matlab can
-users] which tool to use a measure a user-defined angle in a
traj
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it out (b/c matlab can easily ingest column formatted data),
Arneh
Tsjerk Wassenaar wrote:
> Hi Arneh,
>
> I think you're ou
Hi Arneh,
I'd sort of do the same, but would use R (http://cran.r-project.org/)
:) Just a matter of taste (and of sticking to free, open-source
software).
Tsjerk
On 7/17/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it ou
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse
it out (b/c matlab can easily ingest column formatted data),
Arneh
Tsjerk Wassenaar wrote:
Hi Arneh,
I think you're out of luck here. However, this is an excellent
exercise to get started with writing custom made analysis
Hi Arneh,
I think you're out of luck here. However, this is an excellent
exercise to get started with writing custom made analysis tools :)
Alternatively, you could output the coordinates for the C and O using
g_traj and use a script to calculate the angles with the z-axis, in
case it's a single
Hi,
I would use g_bundle with the -z option.
Tom
--On 14 July 2007 10:51 -0400 [EMAIL PROTECTED] wrote:
For instance, I want to measure the angle defined by a carbonyl
vector (a vector going through a C=O bond) in my molecule and the
z-axis of the simulation box.
Not sure if that tool exist
For instance, I want to measure the angle defined by a carbonyl
vector (a vector going through a C=O bond) in my molecule and the
z-axis of the simulation box.
Not sure if that tool exists. You could, however, do this:
1) use make_ndx to make an index group of only the two atoms of interest
2
Hi,
Looking through the gmx tools . . . was wondering, which tool would one
use (if such a tool exists) to measure the fluctuation of a user-defined
angle in a trajectory.
For instance, I want to measure the angle defined by a carbonyl vector
(a vector going through a C=O bond) in my molecul
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