[gmx-users] Regarding 'insolidangle' and some tools

[Teemu Murtola]

Hi,


On Wed, Jul 9, 2014 at 7:13 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> underprot = insolidangle center com of lipids span group "Protein" cutoff
> 5;
>
> I know the purpose of the above statement but I didn't get the meaning of
> some of the words, like "insolidangle" and "cutoff=5". If don't mind, can
> you please explain this statement?
>

Please see 'gmx help selections keywords insolidangle' for a general
explanation. If that is not clear, I can clarify that further.

There are some useful tools for spherical systems like g_jumpdist, g_rdf
> (modified)....etc that you explained in your presentation. Do you have any
> modified gromacs copy with the inclusion of these tools. Because these
> tools are very important for my system. Sorry for such a lengthy mail.
>

I have sent whatever I had for these tools to you personally in May 2013.
Not much has happened since, except that 'gmx distance', 'gmx gangle' and
'gmx sasa' may be able to cover some parts of the needs. Due to various
reasons (most important of which is that I have left academia in 2010), it
has not been exactly fast to get any of those tools actually included in
Gromacs.

I never had "modified Gromacs copy", but only a set of tools and the
selection engine that could be compiled against an existing Gromacs
installation. The selection engine was included in Gromacs 4.5, and the
code has changed a lot since, but the tools have not been updated and so do
not work with newer Gromacs versions without modifications.