[gmx-users] how to determine the box size

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 9 05:40:05 CEST 2010

On 9/07/2010 12:59 PM, 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)

Your conception of the workflow seems a bit confused. If you want to 
minimize your initial configuration before replication, then it is best 
to do that with an .mdp file that turns off PBC. Some reading in section 
7.3 of the manual will (eventually) let you see how to do that - and 
what you don't need to know right now will be useful later. 
Alternatively, make the box size large enough now, do EM.

Then, with the post-minimization structure, pick a box size suitable for 
replication, then use genconf. Then, do whatever you want to do with the 
replicated structure.


> 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?
> 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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