[gmx-users] Number of atoms is very high

[Divya Sunil]

ok..thank you very much

On 26 February 2013 23:54, Justin Lemkul <jalemkul at vt.edu> 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>
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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
##################################