[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110 (How to make carbon nanotube infinite?)
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 20 12:53:23 CET 2009
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
> > in the Carbon nanotube.
> Are there any solvent molecules interfering with the cross-boundary
> No.I use pymol to remove all residues which is far from the egdes 0.7A .
> > >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.
> Blog: http://blog.4message.net
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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