[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110 (How to make carbon nanotube infinite?)

[Justin A. Lemkul]

Cun Zhang wrote:
> Hi, Justin.
> Thank you for your help! I was intended to reply the third question
> after I retryed the simulation under your advice,but I haven't enough time
> to do it. It's too late :)
>  
> Just now, I do a simulation. All seems ok. I will check it again.
> 
> Thank you again!
> 
> Cun Zhang
> 
>      >  >pymol b4em.pdb # I write a python script to remove the SOL
>     molecules
>      > in the Carbon nanotube.
> 
>     Are there any solvent molecules interfering with the cross-boundary
>     bonds?
> 
> 
> No.I use pymol to remove all residues which is far from the egdes 0.7A .
> 
>  

OK.

> 
>      >  >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild
>     the box.
> 
>     Why are you doing this?
> 
> 
> The b4em.pdb generated by genbox have no information about box size. So 
> I use editconf to generate it.
> 

That is not true.  Gromacs can handle a number of coordinate file types, and box 
dimensions are written to the CRYST1 line in the .pdb file.  You should never 
have to re-define your box unless you are doing some very advanced manipulations 
(which you are not, in the case of simply solvating a structure).

>      > NOTE 1 [file CNT.top, line unknown]:
>      >   The largest charge group contains 32 atoms.
>      >   Since atoms only see each other when the centers of geometry of
>     the charge
>      >   groups they belong to are within the cut-off distance, too
>     large charge
>      >   groups can lead to serious cut-off artifacts.
>      >   For efficiency and accuracy, charge group should consist of a
>     few atoms.
>      >   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,
>     CO, etc.
>      >
> 
>     Pay attention to this note.  A charge group of 32 atoms is huge.
>      
> 
> So what's your suggestion about the number of a charge group? 
> 

The note from grompp is quite detailed, and even gives examples of appropriate 
charge group sizes.

-Justin

> 
> -- 
> Blog: http://blog.4message.net

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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