[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

Actually my final .gro file is totally broken into smaller parts when i
load it in vmd, for this what will i do?

On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/9/17 10:05 AM, ISHRAT JAHAN wrote:
>
>> Dear Justin
>> commands which i have used are given belown-
>> gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc
>> -pbc
>> nojump
>> gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc
>> -pbc cluster
>> gmx trjconv -f protein_cluster.xtc -s protein_md.tpr -o protein_pbc.xtc
>> -pbc whole -center -n protein_drg.ndx
>>
>>
> Check the link I provided.  You're going out of order so you're probably
> going to end up with an incorrect representation.
>
> -Justin
>
>
> On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/9/17 1:50 AM, ISHRAT JAHAN wrote:
>>>
>>> Dear all,
>>>> I have done 100ns md simulation of protein with drug using amber99sb.ff
>>>> with gromacs-5.1.4 version. After simulation i found my protein broken
>>>> into
>>>> smaller parts in .gro file but when i load the final xtc file to pr.gro
>>>> molecule does not break. I have applied -pbc nojump ,cluster and whole
>>>> but
>>>> unable to solve the problem.
>>>> Will anyone help me to solve the above problem.
>>>>
>>>>
>>> We'll need to see your commands, exactly as issued, to be able to say
>>> anything. In general:
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions#Suggested_trjconv_workflow
>>>
>>> -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
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>>>
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> --
> ==================================================
>
> 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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