[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110

Cun Zhang apzc2529 at gmail.com
Fri Nov 20 10:36:56 CET 2009

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 .

> >  >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
> 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?

Blog: http://blog.4message.net
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091120/d3d50a9d/attachment.html>

More information about the gromacs.org_gmx-users mailing list