[gmx-users] Number of atoms is very high

[Divya Sunil]

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 <tsjerkw at gmail.com> 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 <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
> Canada
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-- 
"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
##################################