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 <jalem...@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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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