Dear all,
I am performing a MD simulation on a branched polymer through GROMOS 53A6 force field. But, I don't know why when I execute the energy minimization, the system blows up. I have attached the files, and I will be appreciated if anybody can help me.
Regards,
Farideh
Hi,
It is not that hard, actually. Gromacs tools (pretty much) always let you know where are the errors on your system. In your case, going through the em.log file, you can find:
"Maximum force = 8.3360173e+13 on atom 465"
That is a pretty huge maximum force. Check out your em.gro file on VMD or other software and you will actually see the problem. When you do it, you will see that your polymer structure is completelly messed up. The only reason for this is topology error. Double check your topology for bonded terms and non-bonded terms after.
Hope it helps!
Marcelo
ps: topologies are tricky and should be validated. Otherwise, your simulation will have no confidence.
Hi,
It is not that hard, actually. Gromacs tools (pretty much) always let you know where are the errors on your system. In your case, going through the em.log file, you can find:
"Maximum force = 8.3360173e+13 on atom 465"
That is a pretty huge maximum force. Check out your em.gro file on VMD or other software and you will actually see the problem. When you do it, you will see that your polymer structure is completelly messed up. The only reason for this is topology error. Double check your topology for bonded terms and non-bonded terms after.
Hope it helps!
Marcelo
ps: topologies are tricky and should be validated. Otherwise, your simulation will have no confidence.
Hi,
when you generate system, check for nearest distance between atoms and set up minimal distance.
If you have very small distance between atoms, force between them will be very high and simulation (minimization) will blow up.
Check your coordinate input file...may be atoms are too close. You can also try to minimize with a small time step first and if configurations improve then go for larger time step.
- Badges
- Science topic