As Justin hints, using a rhombic dodecahedron would bring the total number of atoms under 1 lakh.
:) Cheers, Tsjerk On Tue, Feb 26, 2013 at 11:50 PM, Divya Sunil <divyasunilku...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
