[gmx-users] Protein break after simulation

[Justin Lemkul]

On 9/9/17 10:12 AM, ISHRAT JAHAN wrote:
> Actually my final .gro file is totally broken into smaller parts when i
> load it in vmd, for this what will i do?
> 

Again, everything you need is in the link I provided.

-Justin

> 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
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
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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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>> Gromacs Users mailing list
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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

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