[gmx-users] Re: How to make carbon nanotube infinite?

[Cun Zhang]

hi, Justin.  Thank you for your meticulous and patient explanation !

Before I see this post, I misunderstood the meaning of sharing bonds.
I thought note only the bonds,but also the angles and the dihedrals
should be added to top file.

It was so complicated to deal manually that I wrote that script.

I will read the doucment you mentioned carefully .
 And I will fix these notes and warnings as grompp and mdrun suggest.


Thank you for your help !

Cun Zhang


> Again, heed the note.  I cannot think of a solid reason for a modern simulation
> being conducted using cutoff electrostatics, unless the goal is to prove that
> such a method is less accurate than a more modern technique like PME.  Again,
> these notes are your friend.  I see that they return during your PR attempts.
> You should not ignore the advice that grompp is giving you.  The artifacts of
> plain cutoffs are well-documented.

> Cun Zhang wrote:
>
> <snip>
>
>> I hope generate sharing bonds between the atoms at the top edge and the
>> atoms at the bottom edge of CNT by x2top. But the parameter -pbc does
>> not work. So I add 4 layers at the top of CNT.pdb and rename it
>> CNT_new.pdb, that is, the front 832 rows of them are same.
>>
>> The  atoms of No. 833-960 in CNT_new.pdb can be seen the bottom 4 layers
>> of atoms of No.1-128 of CNT.pdb translated up a box hight. So after
>> generating the topology file and renaming atoms of No. 833-960 to
>> No.1-128 in the topology file (use the command 'x2top -nopbc') the
>> topology file  of CNT_new.pdb should be the same as the topology file of
>> CNT.pdb with sharing bonds (and angles, diherals) ( use the command
>> 'x2top -pbc' ).
>>
>
> This still makes no sense to me at all.  You're creating duplicate atoms at one
> end of the structure to make them have the same atom numbers of those at the
> other end of the molecule?  Forgive my confusion, I simply don't know what
> you're doing.  The concept of bonding is not that parameters are "shared," it is
> the following:
>
> Consider atoms A and Z, residing at the "ends" of a CNT, as shown here (with
> vertical lines indicating the boundaries of the unit cell):
>
> |                   |
> | A . . . . . . . Z |
> |                   |
>
> You simply need to define a bond in the topology between A and Z, no renumbering
> or fancy tricks required, just add the bond to the [bonds] directive:
>
> [ bonds ]
> ...
> A Z 1
>
> That gives the following:
>
> |                   |
> |-A . . . . . . . Z-|
> |                   |
>
> This bond then spans the periodic boundary.
>
> I'm surprised the EM worked, but I am still unclear on your approach thus far.
>
> <snip>
>
>> 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.
>>
>
> These notes are not simply printed for your entertainment.  If you have a
> 32-atom charge group, you will have potentially severe artifacts, especially if
> you are using cutoff electrostatics, which you are (see additional comments
> below).  Please read in the manual about how to properly define charge groups.
>
> <snip>
>
>> NOTE 2 [file em.mdp, line unknown]:
>>   You are using a plain Coulomb cut-off, which might produce artifacts.
>>   You might want to consider using PME electrostatics.
>>
>
> Again, heed the note.  I cannot think of a solid reason for a modern simulation
> being conducted using cutoff electrostatics, unless the goal is to prove that
> such a method is less accurate than a more modern technique like PME.  Again,
> these notes are your friend.  I see that they return during your PR attempts.
> You should not ignore the advice that grompp is giving you.  The artifacts of
> plain cutoffs are well-documented.
>
> Several other resources to consider using:
>
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> -Justin
>
> --
> ========================================
>
> 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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