[gmx-users] Number of atoms is very high

[Tsjerk Wassenaar]

Hi Divya,

If you set up the box with editconf, the tail cannot have been
outside. It may have looked that way, because the molecules in the box
get wrapped to fit in the rectangular brick corresponding to your
triclinic box. But you should be able to see how there is a hole on
the other side of the solvent where the tail that sticks out fits in.
This is commonly explained in (good ;)) tutorials. If you haven't done
so, please follow one.

Cheers,

Tsjerk

On Wed, Feb 27, 2013 at 9:58 AM, Divya Sunil <divyasunilkumar at gmail.com> wrote:
> 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
> ##################################
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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