[gmx-users] Number of atoms is very high

Divya Sunil divyasunilkumar at gmail.com
Tue Feb 26 23:50:54 CET 2013


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


More information about the gromacs.org_gmx-users mailing list