[gmx-users] Protein break after simulation

[Justin Lemkul]

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.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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