[gmx-users] on the command gmx distance

[Teemu Murtola]

Hi,

On Mon, May 25, 2015 at 7:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 5/25/15 3:48 AM, Brett wrote:
>
>> Suppose I have completed a production MD, and I want to get the distance
>> of
>> OD1 of ASP204 in chain G and NH1 of ARG42 in chain A for the last 5 ns in
>> the
>> MD, will you please tell me the detailed command of gmx distance (how to
>> write the input file and output file in the command) on how to get the
>> distance?
>>
>
> I'm not well versed in the new selection syntax (though it is really quite
> flexible), but this is trivial to do in conjunction with the "old way" of
> making index files with make_ndx and then calling gmx distance:
>
> chain G & r 204 & a OD1
> chain A & r 42 & a NH1
>
> Then just invoke gmx distance -select "com of group x plus com of group y"
> (subbing in x and y as appropriate).
>

The syntax to do this directly with selections is something like this:

"resnr 204 and name OD1 and chain G plus resnr 42 and name NH1 and chain A"

Just pass this to the -select option of gmx distance, and then provide the
appropriate input and output files.

Best regards,
Teemu