[gmx-users] Protein break after simulation
jalemkul at vt.edu
Sat Sep 9 15:35:10 CEST 2017
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.
Justin A. Lemkul, Ph.D.
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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