[gmx-users] how to determine the box size
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 9 05:08:36 CEST 2010
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)
...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.
> 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?
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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