How to prevent Molecules overlapping?

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
Forcefield: gromos54a7

I was able to complete the simulation for 2 separate molecules (C60) and (TAPC) each alone. I want to simulate them together but I fail due to high energy values results from the energy minimization and hence my system fails in step 0 in the nvt equilibiration.

The warnings and errors I receive are below:

WARNING: Listed nonbonded interaction between particles 38369 and 38378
at distance 2.383 which is larger than the table limit 2.137 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Fatal error:
Step 0: The total potential energy is 4.6417e+26, which is extremely high. The
LJ and electrostatic contributions to the energy are 4.6417e+26 and 272701,
respectively. A very high potential energy can be caused by overlapping
interactions in bonded interactions or very large coordinate values. Usually
this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I believe the problem is not in the force field because I am reproducing some papers and I was able to simulate each atom alone, the problem occurs only when I insert the 2 molecules together ad they overlap and the bonds collide with each others. Is there something I can do or write in my command to prevent the overlapping between the 2 atoms ?

Looking forward for any suggestions/recommendations. I can provide any files if needed.

Thanks

2

What did you do to construct the system?

3

I used gmx insert-molecules and I inserted both molecules randomly with ratio 50:50 then energy minimization (but couldn’t lower the energy, it was still high) then nvt equilibiration (failed in step zero due to high energy values)

4

gmx insert-molecules is generally intended for working with small molecules. How many of each species are you inserting? Please provide full commands. What is TAPC, and how large is it? Can it be viewed as a solvent? If so, you should approach construction differently.

5

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&region=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

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6

Your Google Drive link is protected so I cannot access the files. Be sure you don’t have any TAPC confined within the C60. There is no check for this but the program likely can generate such a case. Energy minimization should tell you which atom is experiencing the largest force, so start by simply visualizing the system and look at the area around that atom.