Many Thanks for your reply as usual :)
I have inserted around 500 from each molecule.
I completed the simulation for each molecule alone previously and I was able to insert around 3000 molecule and succeeded to complete the simulation.
I have uploaded all my files in the above link.
The command is as follows:
The insertion was done using script bash 4000.sh which in turn insert randomly the C60 and the TAPC through other scripts C60.sh and TAPC.sh. In this trial I have inserted them in a specific positions trying to form layers however I tried also to insert them randomly in a box but I also received the same error (high energy values).
After the insertion, energy minimization was done but the energy values are very high and hence I failed during step 0 in the NVT equilibiration.
energy minimization was done as below:
home/abdelaal/Desktop/gromacs-2020.3/build/bin/gmx grompp -f minim.mdp -c C60_TAPC_GRM_box.gro -r C60_TAPC_GRM_box.gro -p C60_TAPC_GRM_box.top -o min1.tpr -maxwarn 2
/home/abdelaal/Desktop/gromacs-2020.3/build/bin/gmx mdrun -v -deffnm min1
NVT equilibiration was done as below:
/home/abdelaal/Desktop/gromacs-2020.3/build/bin/gmx grompp -f nvt.mdp -c min1.gro -r min1.gro -p C60_TAPC_GRM_box.top -o nvt.tpr -maxwarn 2
/home/abdelaal/Desktop/gromacs-2020.3/build/bin/gmx mdrun -v -deffnm nvt
TAPC is an organic molecule which is used as a donor in organic solar cell. below are 2 links indicating all the properties of the TAPC and its structure:
https://www.sigmaaldrich.com/catalog/product/aldrich/757284?lang=en®ion=EG
I don’t think it is a solvent. It is a donor which is evaporated with the C60 (acceptor) to form an organic solar cell.
A picture for the C60 and the TAPC is attached.
sorry for the long message, i tried to clarify all the details in addition to the supporting files (complete files and data).
Thanks
