[gmx-users] how to determine the box size

jojo J joojoojooon at gmail.com
Fri Jul 9 04:59:22 CEST 2010

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

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?


On 8 July 2010 01:47, Mark Abraham <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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