[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

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

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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