yes.. I tried both Dodecahedral and octahedral. But in both boxes, the long tail of the protein was outside. Only in cubic, the whole protein is inside. that's why I used that.
On 27 February 2013 09:53, Tsjerk Wassenaar <[email protected]> wrote: > 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 <[email protected]> > 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 [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 > > > > -- > 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 [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 > -- "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
