[gmx-users] PROTEIN FOLDING

[Alexandr Nasedkin]

gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n index.ndx -center

Please read this first:
http://manual.gromacs.org/documentation/2016.1/onlinehelp/gmx-trjconv.html

trjconv is quite powerful, so it worth to know available options.

-Alexandr


On 30/12/2017 16:37, Neha Gupta wrote:
> Hi Justin,
>
> Can you please let me know the exact commands?
>
> None of the commands which I tried are working...
>
> Thanks,
> Neha
>
>
>
>
> On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 12/28/17 8:33 AM, Neha Gupta wrote:
>>
>>> Hi,
>>>
>>> I tried this one
>>>
>>> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
>>> index.ndx
>>>
>>> This asks me to select a group fro clustering and then select a group for
>>> output..
>>>
>>> What should I select first and then next?
>>>
>> Clustering isn't relevant. Your situation is much simpler than it's being
>> made out to be.
>>
>> 1. Make molecules whole
>> 2. Remove jumps
>> 3. Center
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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