[gmx-users] Number of atoms is very high

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Feb 27 09:53:06 CET 2013

As Justin hints, using a rhombic dodecahedron would bring the total
number of atoms under 1 lakh.




On Tue, Feb 26, 2013 at 11:50 PM, Divya Sunil <divyasunilkumar at gmail.com> 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?
> thanks and regards
> Divya
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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