ok..thank you very much On 26 February 2013 23:54, Justin Lemkul <[email protected]> wrote:
> > > 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 > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- "A man is great by deeds, not by birth." ################################## Divya G Nair Senior Research Fellow Bioinformatics Infrastructure Facility Dept:of Biotechnology and Microbiology Kannur University Kannur,Kerala,India-670 661 Phone: +91 9495112169 ################################## -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
