[gmx-users] i have a question about multiple chain simulation at the same box

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 02:01:54 CEST 2018

On 9/5/18 9:25 AM, milad bagheri wrote:
> I'm going to examine the interaction between the two proteins using
> molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1
> from the rcsb , which has two protein(Complex). I want to create a gap
> between two protein, and then with the same coordinate Put these two
> proteins in a box and run MD 100 nanoseconds, for validation this trick
> compare rmsd x-ray pose and Md pose.
> please help me ...

Separate the coordinates of the two proteins, translate one of them with 
editconf, and concatenate the new coordinates back together.



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


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