Hello, my dear friends!
@dexterdev is back after a long gap.

Today I will discuss on creating *infinite* molecular structures for MD simulations!!! (**Sounds impossible task... Right?**)

In MD(molecular dynamics) forums etc, you will find these queries very often. For example:
- See this research gate link: [How to create an infinite graphene sheet with proper periodicity?](https://www.researchgate.net/post/How_to_create_an_infinite_graphene_sheet_with_proper_periodicity). 
- Another link from namd-l forums: [Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC)](https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/3141.html)

So I thought why not document this problem with a solution on STEEM blockchain.

There are times when you require to create infinite molecular structures("infinite" in the sense that the molecules in one simulation cell are covalently bonded at the interface to the respective molecules in the adjacent periodic images) in MD simulations. For example, if you want to learn how a DNA chain or protein interacts with a Carbon nanotube, you may want to keep this particular nanotube structure span whole periodic cells. It seems impossible at first sight. But there are some hacks through which we can create such structures. I will explain this in the context of VMD and NAMD softwares. As I have explained in my previous articles, VMD is a visualization software for molecular dynamics(MD) trajectories and NAMD is a MD engine.

![](https://i.imgur.com/Jtl1xHd.gif)<center>
*Different periodic images of an all-atom simulation system, where the carbon nanotube(cyan) technically spans infinitely(in the sense the nanotube is covalently bonded at the interface of different periodic images) in the z-direction(blue axis). The white transparent box is waterbox and the purple molecule is a protein.*</center>


## Repository

https://github.com/dexterdev/STEEMIT/tree/master/INFINITE_CNT

## What will I learn?

You will learn how to set up a molecular dynamics system where molecular structures should extent in its periodic cells infinitely. 

**Softwares used:** VMD, NAMD
**Necessary Plugin for connecting bonds between periodic images:** [topotools](https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/)
(Topotools comes with latest versions of VMD)
If you are not familiar with VMD and NAMD etc, please follow my past articles. Links in **References**.

## Difficulty

Intermediate

## System

**The System comprises of:** 
- Carbon nanotube(armchair CNT(5,10)) 
(5,10) are [chirality numbers](http://www.photon.t.u-tokyo.ac.jp/~maruyama/kataura/chirality.html). It is of no significance here for this article.
- Aβ [intrinsically disordered protein](https://en.wikipedia.org/wiki/Intrinsically_disordered_proteins)(from [1Z0Q.pdb](https://www.rcsb.org/structure/1z0q)) 
- Waterbox with TIP3P water model 
- NaCl ions with concentration 150mM/litre to neutralize the total charge in system

## Tutorial Content

This tutorial is broken down into the following sections:
- Creating CNT psf,pdb files using Nanobuilder VMD plugin
- Adding the IDP(intrinsically disordered protein) to the system and positioning it properly
- Adding Waterbox and ions
- Using topotools to modify the structure by adding bonds in CNT C atoms between self and periodic image
- Equilibration RUN setup
- Verifying Carbon bonds between self and periodic cell are functioning properly

## Creating CNT psf,pdb files

This is pretty straightforward. Open `Carbon Nanostructure builder` tool from VMD>Extensions>Modeling. 

![](https://i.imgur.com/itvqXWN.png)

Choose CNT options accordingly. Chirality numbers and length of tube etc. Once the structure is created, create the pdb psf files using:

```
animate write pdb CNT.pdb
animate write psf CNT.psf
```

in VMD Tk console.

## Adding the IDP to the system and positioning it properly

The IDP structure can be downloaded from PDB databank([LINK](https://www.rcsb.org/structure/1z0q)). The PDB id is 1Z0Q. Load the CNT structure and you can position the loaded IDP wherever appropriate(VMD hotkey for moving molecule is `8`). Merge the structures in VMD. Save the merged structures. 

## Adding Waterbox and ions

```
package require solvate
solvate ./OUT.psf ./OUT.pdb -minmax {{-30.56800079345703 -11.4019999504089355 0.0} {40.322999954223633 47.20600128173828 119.11799621582031}} -o OUT_water -s WB
```

The above script can be used to add water. Change the coordinates appropriately. Add ions using Autoionize from here VMD>Extensions>Modeling.

## Using topotools 

There is a major issue in the structure we have created now. The CNT terminates at box edges of the "self" simulation cell. Which means there is a minor gap between this structure and the CNT in the next periodic cells. Topotools can be used to modify the structure by adding bonds in CNT C atoms between self and periodic images.

![](https://i.imgur.com/MEeMaGM.png)
*(self-red,periodic-green. See there is no bond between red and green tubes, which can create unnecessary artifacts.)*


![](https://i.imgur.com/8WrE0WH.png)
*(The distance between the "supposed to be" carbon-carbon bond, is lesser than the usual 1.4 Angstroms.)*

So how do we create infinite CNT is the question. There is a hack possible with the aid of topotools. Topotools can create bonds between atoms. The format is as below:

```
package require topotools
topo addbond $atom-index1 $atom-index2
```

For example in the above figure, we need a bond between atom 22 and 1403. The respective atom indices are 21 and 1402.

```
topo addbond 21 1402
```

You do this for the multiple selections. To make things easier in terms of getting at least the required atom indices, you can use the below selection commands(The selections lie in the 0.9 Angstrom edges of the nanotube):

```
set sel [atomselect top “segname TUB and z<0.9”]
$sel get index
set sel [atomselect top “segname TUB and z>122.5”]    
#(118.2 = 123.2-0.9)
$sel get index
```

After applying that topo command, let us see the image:
![](https://i.imgur.com/15tyEVs.png)

It seems like something has gone wrong. The bond went in between self molecules rather than between self and periodic cell. This problem which is a VMD rendition one will persist in our simulation. But we can verify if there is a proper bond between self and periodic cell structure by running a small simulation. We will come to that section later.

## Equilibration RUN setup

```
structure          ./OUT_water_ionized_bondcorrection.psf
coordinates        ./OUT_water_ionized_bondcorrection.pdb

set temperature    298
set outputname     test


firsttimestep       0


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm      on
parameters           ./par_water_ions.prm
parameters           ./par_nanotubes.inp
parameters           ./par_all36_prot.prm

temperature         $temperature

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        15.0
margin               8.0

# Integrator Parameters
# fullElectFrequency*timestep <=4.0
# stable time steps:
#       with rigidBonds=all: electro:6fs;short-rangeNB:2fs;bonded:2fs
#       otherwise          :         2fs               2fs        1fs
timestep            2.0  ;# 2fs/step
rigidBonds         all  ;# Needed for 2fs steps
useSettle           on
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10
zeroMomentum        yes


# Constant Temperature Control
langevin            off    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

#temperature coupling for temperature coupling
tCouple             on
tCoupleTemp         $temperature


# Periodic Boundary Conditions
# center of the periodic box; NOT ORIGIN!!!
cellBasisVector1 71 0 0
cellBasisVector2 0 68 0
cellBasisVector3 0 0 124
cellOrigin 10.136194229125977 18.867944717407227 61.83677673339844
#add appropriate numbers at # above

wrapAll             on


# PME (for full-system periodic electrostatics)
# multiples of 2,3,5 & >=dimensions above
PME                 yes
PMEGridSizeX        90
PMEGridSizeY        90
PMEGridSizeZ        150
#add appropriate numbers at # above

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston       on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    $temperature


# Output
outputName          $outputname

restartfreq         50000           
dcdfreq             10000                
xstFreq             10000
outputEnergies      10000
outputPressure      10000

#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization
minimize            5000
reinitvels          $temperature

run 111000  ;# 222ps
```

## Verifying Carbon bonds between self and periodic cell are functioning properly

To verify the topotools hack, we can check the the evolution of carbon-crbon bonds in the CNT at the interface. Between our indices 21 and 1402, the bond distance starts at 1.07 Angstroms. It spikes to 1.57 at minimization and evolves towards 1.44 which is great! Now once you feel the system is equilibrated, you can restart the simulation with fixing the CNT atoms in simulation setup.

![](https://i.imgur.com/RFZY8OS.png)
*The above figure shows the evolution of C-C (between 21 and 1402 indices) bond distances w.r.t time. The time we simulated for is around 222ps. See the distance between carbon-carbon bonds saturating towards 1.44-ish Angstroms, which is what we need.*

![](https://i.imgur.com/DwEt8Cu.gif)
*(Evolution of distances - A gif.)*

## Necessary Files

All necessary files are uploaded in Github. 
LINK: https://github.com/dexterdev/STEEMIT/tree/master/INFINITE_CNT


## References
### My previous posts:
To learn about VMD and PDB file format, see here:
- https://steemit.com/steemstem/@dexterdev/visualizing-bio-molecules-in-computer-part-1-let-us-inspect-a-pdb-file-and-see-it-using-vmd
- https://steemit.com/steemstem/@dexterdev/visualizing-bio-molecules-in-computer-part-2-introduction-to-tcl-scripting-environment-in-vmd-1-sbd-prize-task-inside

To learn about the concepts in All-atom molecular dynamics see articles below:

- https://steemit.com/steemstem/@dexterdev/classical-molecular-dynamics-series-part-1-the-fundamentals
- https://steemit.com/steemstem/@dexterdev/classical-molecular-dynamics-series-part-2-the-force-field
- https://steemit.com/steemstem/@dexterdev/classical-molecular-dynamics-series-part-3-solving-the-molecular-dynamics-equation

To setup and run simulations in NAMD software, see below:
- https://steemit.com/steemstem/@dexterdev/classical-molecular-dynamics-series-part-4a-let-us-setup-a-simulation-and-run-it
- https://steemit.com/steemstem/@dexterdev/classical-molecular-dynamics-series-part-4b-running-small-systems-on-your-computer
- https://steemit.com/steemstem/@dexterdev/let-us-cool-dmpc-bilayer-lipids-an-18-day-long-molecular-dynamics-experiment-on-hpc-facility

### Textbook references for learning theory of Molecular Dynamics:

- "Statistical Mechanics: Theory and Molecular Simulations" by Mark E. Tuckerman
- "Molecular Modelling: Principles and Applications" by Andrew R. Leach
- "Computer Simulation of Liquids" by D. J. Tildesley and M.P. Allen

### References specific to NAMD and VMD:

- [NAMD userguide](http://www.ks.uiuc.edu/Research/namd/cvs/ug.pdf)
- [NAMD tutorial](http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf)
- [VMD userguide](http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug.pdf)
- [VMD tutorial](http://www.ks.uiuc.edu/Training/TutorialsOverview/vmd/vmd-tutorial.pdf)




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