[gmx-users] regarding editconf

[Justin Lemkul]

On 1/15/19 7:46 AM, Ali Khodayari wrote:
> Dear users,
>
>   
>
> I am trying to reorient and re-center my solute using editconf. Performing
> such I can place the structure at the desired place, yet it is outside the
> box when I visualize it in VMD. It leads to an error after mdrun complaining
> about a water molecule not being settled.
>
> Here is the command I use:
>
> $ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c
> -center 0 0 0 -rotate 0 350 0 -n ndx.ndx
>
> Do you see where the problem is?

First, there is no such thing as "outside" an infinite box, so that 
should not be the cause of any actual problem.

Regarding editconf, you're doing too many things at once, which may be 
mutually exclusive, so you may not be getting what you want. You're 
telling editconf to align the longest axis along x (with -princ) but 
also to rotate about y (-rotate 0 350 0). Don't do both of those at once.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================