[gmx-users] conversion of a trajectory from .trr to .gro

[gangotri dey]

Dear Justin and Dash,

Thank you for the kind response.
I have another related problem. My xtc file is huge ~ 15 GB as I ran my
calculation for 5 ns in a big box. I can convert the .xtc to .gro but I
would like to do it in parallel using the cluster as it ran for a long time
when I used the head node.
However, when I use the below syntax and submit the job to the queue it is
asking for a group index that I do not know how to provide when using the
cluster to run the job.

gmx_mpi trjconv -s *.tpr -f *.xtc  -o conf.gro -sep

In this case, what should I do please?


*Thank you*

*Gangotri *




On Mon, Sep 18, 2017 at 7:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/18/17 4:18 PM, gangotri dey wrote:
>
>> Hello!
>>
>> I would save it in vmd all at once but I would like to ideally save it in
>> separate files. Also, the trajconv statement did not work.
>>
>>
> Your original error will be solved by passing a .tpr file to trjconv -s,
> as suggested below.  If you want to save intervals of time into separate
> files, use -b and -e.
>
> -Justin
>
>
>> *Thank you*
>>
>> *Gangotri *
>>
>>
>>
>>
>>
>> On Mon, Sep 18, 2017 at 3:08 PM, R C Dash <rcdash0910 at gmail.com> wrote:
>>
>> Open you the gro file in VMD. Add load data and show the trr or xtc file.
>>> right click on to it and save coordinate. File type. gro.
>>> or
>>> trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro
>>>
>>> RC Dash,
>>>
>>>
>>> On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey <holyriver6 at gmail.com>
>>> wrote:
>>>
>>> Dear all,
>>>>
>>>> I would like to transform my trajectory file n.trr or n.xtc to n.gro
>>>> after
>>>> my production run. I have used trjcat and trjconv to transform it using
>>>> the
>>>> index file. But in both the cases, it says "Can not write a gro file
>>>> without atom names". How can I transform it please?
>>>>
>>>>
>>>>
>>>> *Thank you*
>>>>
>>>> *Gangotri *
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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