[gmx-users] Number of atoms is very high

Justin Lemkul jalemkul at vt.edu
Tue Feb 26 23:54:06 CET 2013

On 2/26/13 5:50 PM, Divya Sunil wrote:
> Hello
> I have a protein consists of 2303 atoms. I simulated it in water using
> cubic box. As the protein has a long tail, the no. of water molecules to
> fill the box is very high (132235). After simulation I converted the .gro
> file to .pdb and in which I have seen that the atom number after 1 lakh is
> again started to denote as 1 and also the molecule number after 9999 as 1.
> So in this system there are 4 molecules that have number 1. Is this create
> any problem during simulation/ before simulation? ( I noted this only after
> simulation and the system was not hanged) Also is it possible to remove
> some water molecules manually after adding solvation to reduce the number
> of atoms?

There is no problem during the simulation, and the fact that atom numbering 
starts over is simply a limit of PDB format.  Proper representations can 
probably be obtained using other file formats.  Theoretically, there may be 
issues with creating index groups, but likely only if dealing with water, and 
these issues can again likely be overcome by choosing a different file format.



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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