[gmx-users] Number of atoms is very high

[Justin Lemkul]

On 2/26/13 6:37 PM, Divya Sunil wrote:
> ok..thank you very much
>

The other thing I forgot to mention is that perhaps you can use a different box 
shape.  Dodecahedral and octahedral require a lot fewer water molecules than a 
cubic box of equivalent periodic distance.

-Justin

> 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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>

-- 
========================================

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

========================================