[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110
apzc2529 at gmail.com
Fri Nov 20 10:36:56 CET 2009
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!
> >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 .
> > >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.
> 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
> > 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
> > 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?
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