While trying to run MD simulation for 50ns, i got some errors read as
"WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000
WRITING COORDINATES TO DCD FILE output.dcd AT STEP 500000
WRITING COORDINATES TO RESTART FILE AT STEP 500000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 500000
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 500000 TO 310 KELVIN.
TCL: Running for 25000000 steps
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 500000 1758.0188 1801.9004 2376.2868 32.0673 -57791.6942 4645.6399 0.0000 0.0000 12929.5296 -34248.2515 314.2067 -47177.7811 -34247.2801 314.2067 -547.9328 -2890.9435 156892.4304 -547.9328 -2890.9435
ERROR: Atom 4439 velocity is 4671.87 1153.77 2833.69 (limit is 5000, atom 327 of 328 on patch 18 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 18 pe 1).
FATAL ERROR: Exiting prematurely; see error messages above.
FATAL ERROR: Exiting prematurely; see error messages above."
The error happens just after minimzation is complete and the running for 25000000 steps just started. Any recommendation to solve this problem?
One of the simplest things that you can try is to reduce the time step that you are using for your simulation. If you are using a Verlet or similar algorithm it is the first thing can try because a too large time step can negatively affect the stability of the MD run.
Regards!
I have tried by decreasing the timesteps. I have attached my algorithm. Please have a look
It seems that the minimization process was not enough. And also could be because of a really compact system, so the time step has not been chosen correctly.
I have encountered this problem while ago. I have tried these two methods: 1. Did a longer minimization process. and at the same time 2. used a smaller time step. It has been solved. After a while, the system got stable, so I increased the time step up to 2 fs. you can try this method. Hope it works for you.
My time step is 2fs and i did minimization for 1ns and the run time is 50ns. I also tried decreasing time step but encountered same problem
You meant that your MD simulation even did not start the run-equilibration process? you immediately got an error just after minimization was complete?
If that's the case, choosing a smaller time-step will not help you, it means the system has not even started solving the equation of motions.
Yes, i got error just after completing minimization run i.e, error is shown as soon as MD run-equilibrstion starts. So how will i solve this problem.?
I have checked your .namd file, it seems perfectly fine to me. Maybe there is something wrong with the system... .
Anyway, There are some solutions to the same error in namd-list or in RG:
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0908.html
https://www.researchgate.net/post/unstable_MD_system-rattle_algorithm_error_at_a_particular_atom_How_to_go_about_it
Also try them. Hope one of them will work for you.
The reason for atoms moving too fast even in 2fs as time steps may be due to two issues. First, the number of atoms in the file is so large that the simulation could not be processed. Second the distance between atoms is so short that reducing the time step to even 2fs is not enough for the system to calculate the required parameters.
You can try using coarse-grained or modifying the molecules' structure to better fit the simulation.
- Badges
- Science topic
- Similar topics
- Filing