[gmx-users] about how to create angle.index with specific angles

[Justin Lemkul]

On 4/30/20 2:07 PM, lazaro monteserin wrote:
> Dear Dr. Lemkul I did it. It works. Thank you very much for the advise.
>
> Now I am having issues opening the (.xpm) files generated that contain for
> example the gibbs energy landscape on the two first eigenvectors of the
> dPCA.
>
> If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps"
> it write this error: "Input error or input inconsistency:
> Invalid XPixMap"
>
> Do you know if I am missing something here? Do I have to install something
> in my OS to be able to see .xpm images?

The error is coming from xpm2ps which means there's something wrong with 
the .xpm file itself but without seeing how you generated it (exact 
command and description of how you prepared the input data file) and 
perhaps the .xpm file itself (uploaded somewhere), it's impossible to 
comment further.

-Justin

> Thanks in advance,
>
> Lazaro
>
> On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 4/29/20 7:11 PM, lazaro monteserin wrote:
>>> Dear Dr. Lemkul it could be possible use that angle.index with the
>> selected
>>> dihedrals written by hand as index file for gmx angle for dihedral
>>> Principal Component Analysis?
>> You can create index groups however you like for whatever analysis you
>> want to perform.
>>
>> -Justin
>>
>>>    Kindly,
>>> Lazaro
>>>
>>> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 4/29/20 5:01 PM, lazaro monteserin wrote:
>>>>> Dear gromacs users,
>>>>>
>>>>> Is there any way to tell gmx mk_angndx to create the index file with
>>>>> dihedral angles from a (.tpr) for specific atom numbers (atom level,
>> e.g
>>>> 1,
>>>>> 2, 3) from my molecule?
>>>> mk_angndx is designed for distributions of similar angles (e.g.
>>>> evaluating force field sampling). If you want to compute specific
>>>> angles, use make_ndx or simply write the index groups by hand.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================