Hey,
For the average distance matrix, you can use g_rmsdist.
Cheers,
Tsjerk
On Mon, Apr 15, 2013 at 6:19 PM, Justin Lemkul 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 e
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 bet
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 o
Thank you for this.
Steven
On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul wrote:
>
>
> On 4/15/13 11:08 AM, Steven Neumann wrote:
>>
>> On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 4/15/13 10:06 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:01 PM
On 4/15/13 11:08 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul wrote:
On 4/15/13 10:06 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul wrote:
On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distan
On 4/15/13 11:17 AM, Steven Neumann wrote:
And another question: I want to analyze all 5 nanoseconds every 20 ns
of my trajectory. Would you suggest using trjcat to create one
trajectory first and then process to g_mdmat or can I specify time
periods (frames) I wish to analyze?
You have to c
And another question: I want to analyze all 5 nanoseconds every 20 ns
of my trajectory. Would you suggest using trjcat to create one
trajectory first and then process to g_mdmat or can I specify time
periods (frames) I wish to analyze?
Steven
On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann wrote
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul wrote:
>
>
> On 4/15/13 10:06 AM, Steven Neumann wrote:
>>
>> On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distance matr
On 4/15/13 10:06 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul wrote:
On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distance matrix of each amino acid (1, 2, ...25)
averaged over simulation time with all amino acids. So matrix
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul wrote:
>
>
> On 4/15/13 9:59 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I want to calculate a distance matrix of each amino acid (1, 2, ...25)
>> averaged over simulation time with all amino acids. So matrix of
>> 25x25:
>>
>> 1) is there a
On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distance matrix of each amino acid (1, 2, ...25)
averaged over simulation time with all amino acids. So matrix of
25x25:
1) is there a tool which can do this or just the use of g_dist fof 600
(25x25 - 25) times?
2
Dear Gmx Users,
I want to calculate a distance matrix of each amino acid (1, 2, ...25)
averaged over simulation time with all amino acids. So matrix of
25x25:
1) is there a tool which can do this or just the use of g_dist fof 600
(25x25 - 25) times?
2) Would you recommend any nice visualisation t
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