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
--
========================================
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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