How to build this molecule structure?

[donmbringer]

The molecule is put in the attachment. I tried to build it by insert benzene and repeat replacing H by C and adding H again, but VNL reports error.

What is the correct way to build it?

[Anders Blom]

Without being careful about the C=C bond length, I did this:

1. Insert benzene
2. Measure distance between H on opposite sides, it's about 5 Å
3. Open Coordinate Tools>Translate
4. Tick "Copy", enter 6 Å for y, and click Translate twice
5. Change the relevant H to C and S

Now the molecule is pointing along Y; to make it along Z, open Move Tool, select the two S atoms and enter 0,0,1 for r1-r0.

It remains to think a bit about the C=C bond length, or optimize the structure with DFT.

[donmbringer]

Hi Dr Blom,

I have successfully built the model in your method, thank you.

I build the molecule junction by repeating the method of tutorial with this molecule (-S terminated, the same as tutorial), and I just repeat the exact same process to simulate the I-V properties of this junction using the same parameters sa tutorial. The only parameter I changed it that I set the lattice parameter in C direction to be 70 rather than 45, to make it long enough for my molecule.

I successfully get the device transmission spectrum. However, unfortunately, when I run the program to simulate the I-V curve (Chapter 4 in tutorial), it always stop at the beginng (pro1.jpg, attachment) and reply the error (pro2.jpg).

I have simulated some other molecule junction before, but this is the first time I face this problem. I tried to, for example, turn the benzene ring by 90 degree, and simulate again, but the same error happens.

Could you please give me a hand?

[Anders Blom]

Looks like a memory error, do you have enough RAM in the computer?

[donmbringer]

So, does it mean the RAM in my computer is not big enough for this simulation?

[Anders Blom]

Could be, yes. We have been working on a way to estimate the memory usage of a system, it's a bit rough, but at least gives some idea. How much do you have?

[donmbringer]

My computer has 3 Gb RAM. This is still not enough for this simulation?! Wa....

[Anders Blom]

Well, if your system has 4000 atoms, 3 GB is not a lot. And I have no idea how large your system is...

[donmbringer]

It is just the molecule I showed above and then sandwiched between two gold electrodes (similar to the tutorial, which is exactly the same with the tutorial, except for the molecule, which is originally benzene in tutorial then replaced by my molecule here).

[Anders Blom]

3 GB is reasonable, but as always it also depends on which other programs are running, esp. on Windows. Or the error may be completely different - is it reproducible? The reason I'm pushing you with many questions is that things are so much easier on our side if we have all information, which means the input script, the method of running, the system specs, and not least if the error only occurred once or every time. I can say in general I have not seen the type of error box you showed, so it may have been spurious.