[gmx-users] Re: DNA simulations

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 9 22:11:21 CEST 2012

On 7/9/12 4:07 PM, SatyaK wrote:
>   Hello,
>   I followed below steps using VMD and GROMACS but something went wrong in
> using GROMACS which I am not able to figure out. Appreciate your help.
>   1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2
>   2. VMD: within 5 of nucleic
>               $sel writepdb initialfile_updated.pdb
>               $sel delete
>        (initialfile_updated.pdb has only those molecules that are at a
> distance of 5A)
>   3. I used GROMACS to convert back to .gro:editconf -f
> initialfile_updated.pdb -o initialfile_updated.gro -d 0.2
>   The coordinates in ininitialfile.gro and initialfile_updared.gro are
> different. I quite don't understand the reason for the same.

You are resetting the box by invoking the -d option with editconf.  If 
initialfile.gro had all the original atoms and initialfile_updated.gro has 
significantly fewer (due to the selection made in VMD), then the size associated 
with the system is much smaller.  Using -d re-centers the system within the 
defined box, thus shifting the coordinates.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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