[gmx-users] simulation box

[Lucio Montero]

If you use periodic boundaries, the box size needs to be more than twice the 
cutoffs, to avoid calculation errors. I found this advice in the manual. (I 
though reading it was a time waste, but more time I was going to waste doing 
a wrong 1 ns simulation on a big system).

--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Tuesday, March 03, 2009 12:00 PM
To: <rsoares at fcfrp.usp.br>; "Discussion list for GROMACS users" 
<gmx-users at gromacs.org>
Subject: Re: [gmx-users] simulation box

> Quoting Ricardo Soares <rsoares at fcfrp.usp.br>:
>
>> noob noob wrote:
>> >
>> > Dear all,
>> >
>> >  I am new about MD simulation and I have some questions about the box
>> > size.
>> >
>> > I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5
>> > nm ) but now I change to a bigger molecules and increase the number of
>> > molecules. So,the new system cannot fix into the previous box.
>> > Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm
>> > x 20 nm) which can fix the system nicely.
>> >
>> > So, is it compulsory to use certain box size in our system? or we just 
>> > use
>> > any box size which our molecules can fix into it, then perform MD?
>> >
>> Sorry, I didn't see this other question of yours.
>> If you use a box that is much larger than the main molecule, you will
>> need lots of water, which will be time-consuming. Otherwise, if you use
>> a very small box, it may compromise the free movement of the protein.
>> So i say the best option is to scale the box size according to your
>> specific molecule size. This is done within the editconf program. (see
>> the gromacs manual for further reference).
>>
>
> In addition, you need to consider cutoff lengths and periodic boundary
> conditions/minimum image convention.  Some textbook reading is in order.
>
> -Justin
>
>> Cheers,
>>
>> Ricardo.
>>
>>
>> > Sorry for the "stupid" questions.
>> >
>> > thanks for the comments.
>> >
>> >
>> > Alvin Chan.
>> > ------------------------------------------------------------------------
>> > check out the rest of the Windows LiveT. More than mail-Windows LiveT
>> > goes way beyond your inbox. More than messages
>> > <http://www.microsoft.com/windows/windowslive/>
>> > ------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>> --
>> ___________________________________________________________
>>
>> Ricardo Oliveira dos Santos Soares
>> Post-graduation Student in Biological Physics
>> University of Sao Paulo - USP
>> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>> Phone: 55 (16) 3602-4840
>> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
>> ___________________________________________________________
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php