Tips fo pewald3D calculation based on crystal structure

[Paul Hume]

Hi 

I'm a new user of VOTCA, and I'm trying to use the pewald3d calculator for applications in OPV (I have a crystal structure that I'm trying to feed into VOTCA).

Almost everything seems to be working, except I'm not sure how to prepare my system morphology (a triclinic crystal) with a cubic box, as VOTCA requires.

I'm wondering if anyone would be able to share a way of doing this? 

My background is more in quantum chemistry, rather than MD, so I have my fingers crossed that there's an easy way of doing this :)

Thanks very much,

Paul

[Denis Andrienko]

Hi Paul,

In principle VOTCA understands triclinic boxes (except the Kinetic Monte Carlo part). Let us skype (crionez) and see if I can help you with specific questions. Anastasia Markina (in cc) did a lot of OPV simulations recently, but she is on a holiday at the moment - working remotely.

Best,
Denis

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[paulalex...@gmail.com]

Hi Everyone

We resolved this via email, but I'll post the solution in case it's helpful to anyone else.

Most of the calculators in VOTCA are compatible with triclinic boxes (aside from the KMC part).

My problem was that I was using a pdb file that contained unit cell information for my system geometry.

When I ran the command ctp_map -v -t topol.tpr -c test.pdb -s system.xml -f state.sql, I got the following error:

an error occurred:
Non cubical box in pdb file not implemented, yet!

The solution was just to convert my .pdb to a .gro file instead. So I just used the editconf command in Gromacs (specifying my particular periodic boundary conditions).

The calculator then runs fine :)

Thanks again for your help Denis and Anastasia,

Paul