[gmx-users] how to determine the box size

[Justin A. Lemkul]

jojo J wrote:
> Hello Mark,
> 
> Thank you for your reply. AS for the steps you mentioned to solvate a 
> molecule: I have a simple molecule replicated by genconf -nbox in one 
> direction. When I try to energy minimize this single molecule grompp em 
> gives error: rlist is longer than half box size or longer than shortest 
> diagnal boz size... I increase the size and everything is fine but can 
> you please tell me what is the criterion to specify the size. Does 
> boxsize affect results in MD? ( I am asking this because if I want to 
> use genconf to replicate this molecule which is in a large boxzise the 
> final size of the system can become very large so I have to use  
> editconf to reduce the size again)
> 

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

...and perhaps some textbook reading.  If you make a system too small, you'll 
waste a whole lot of time generating meaningless trajectories.

> Also sometimes some parts of the molcule in the box are outside the box 
> when I see the trajectory (ngmx) at the beginning.. and I think because 
> of the pbc it jups inthebox from the otherside. Should the particle be 
> entirely in box at the beginning? 
> 

Depends on how you set it up.  In the absence of the actual commands you used, 
there's no way to know whether you've positioned your molecule properly.

-Justin

> Thanks,
> 
> On 8 July 2010 01:47, Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
>     Please start new emails for new discussion topics. That way you
>     increase the chance that people with the interest and expertise can
>     use their time efficiently, and that you get an answer. Also,
>     archives work better if you separate topics.
> 
>      > Please Let me ask two more simple questions about solvating a
>     molecule. I am using genbox to solvate a solute. I have solute.gro
>     and solvent.gro. What should be the dimension of box in solvent.gro
>     if i want to put -nmol numbers in the solute box. Does it matter
>     what size the box of solvent is (last line in gro)?
> 
>     I don't think you are using the right tool for your problem, but
>     your description is so opaque it's hard to tell. genbox -nmol will
>     try to fill interstices, which need to exist for it to do any good.
>     That means you need to have prepared your solvent.gro with your
>     solute in mind.
> 
>      > I have solvated the solute with 50 moleecules of solvent. I have
>     the structure file obtained from genbox. To run em or MD I need to
>     have top file. so I am using pdb2gmx and I get a top file for the
>     solute and 50 solvents but I have one moleculetype (named protein by
>     default). I am confused If I need to have 2 molecuels types for
>     solute and solvent, also if I need to enter the number of solvent
>     molecules at the end of the top file [mols] option, or what I have
>     now is fine and I can proceed to em and md usuing mdp files? :)
> 
>     1. use pdb2gmx on an unsolvated .gro to get your protein .top
>     2. use editconf to set the simulation box how you want it
>     3. use genbox -p to add solvent and take care of modifying your .top
>     (unless your solvent is not water, in which case you'll probably
>     have to do some manual editing of your .top)
>     4. grompp and mdrun
> 
>     Perhaps doing some tutorial material will make this and other
>     workflows more readily understood?
> 
>     Mark
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> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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