[gmx-users] Peptide distance matrix

[Tsjerk Wassenaar]

Hey,

For the average distance matrix, you can use g_rmsdist.

Cheers,

Tsjerk


On Mon, Apr 15, 2013 at 6:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/15/13 12:08 PM, Steven Neumann wrote:
>
>> And last question:
>>
>> Are these minimum distances averaged over the simulation time? Cannot find
>> any equation the way it is calculated... in Manual its written:
>>
>> This minimum distance between two residues Ai and Aj is defined as the
>> smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output
>> is a symmetrical matrix of smallest distances between all residues.
>>
>> And nothing else...
>>
>>
> The question is answered by reading g_mdmat -h.
>
>
> -Justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.