From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Wed Dec 02 2020 - 13:43:17 CST
Hello NAMD community,
I am having an issue with a system containing a protein, lipid, water, and ions (totaling ~50,000 atoms). I built the system using CHARMM-GUI and I am having difficulty with the simulation failing in the transition from minimization to equilibration. Consequently, I could use a bit of guidance.
I first attempted to minimize the system with the protein backbone and ions held fixed, except for a small portion of the protein which was not held fixed. This was done with fixedAtoms and the minimization was performed for 2000 steps at a 2 fs timestep and at a temperature of 310 K. However, the simulation failed at the start of the equilibration with the error 'ERROR: Constraint failure in RATTLE algorithm for atom XXXX!'. I checked the output and the atoms in question seem to be fine. The NAMD archives suggested that this error was caused by insufficient minimization and/or not using a 1 fs timestep (Or maybe due to rapid heating?).
As such, I restarted the simulation with an additional 5000 steps of minimization (all other simulation parameters unchanged). Again, the minimization successfully completes but fails at the start of the equilibration step this time with the following:
namd2:11843 terminated with signal 11 at PC=110c1ea SP=7eba4bffd2c0. Backtrace:
namd2(_ZN12PmeRealSpace14compute_forcesEPKPKfPK11PmeParticleP6Vector+0x620)[0x110c1ea]
namd2[0xc68efc]
namd2(_ZN19CkIndex_WorkDistrib29_call_enqueuePme_LocalWorkMsgEPvS0_+0xe)[0x11fe2fe]
namd2(_Z15_processHandlerPvP11CkCoreState+0x543)[0x132dba3]
namd2(CsdScheduler+0x59f)[0x14c0b5f]
namd2[0x149c5ff]
namd2[0x1497f63]
/lib64/libpthread.so.0(+0x7dd5)[0x7efe03b65dd5]
/lib64/libc.so.6(clone+0x6d)[0x7efe0136b02d]
This error was not as clear, at least to me, and my search into this termination seems to suggest the issue is with the program trying to access unassigned memory.
So, I next decided to restart the simulation with an additional 3000 steps however with a 1 fs timestep (all other simulation parameters unchanged). Again, the minimization successfully completes but fails at the start of the equilibration step with a similar termination as above:
namd2:1714 terminated with signal 11 at PC=110c1ea SP=7efd3c76a1c0. Backtrace:
namd2(_ZN12PmeRealSpace14compute_forcesEPKPKfPK11PmeParticleP6Vector+0x620)[0x110c1ea]
namd2[0xc68efc]
namd2(_ZN19CkIndex_WorkDistrib29_call_enqueuePme_LocalWorkMsgEPvS0_+0xe)[0x11fe2fe]
namd2(_Z15_processHandlerPvP11CkCoreState+0x543)[0x132dba3]
namd2(CsdScheduler+0x59f)[0x14c0b5f]
namd2[0x149c5ff]
namd2[0x1497f63]
/lib64/libpthread.so.0(+0x7dd5)[0x7f04c6b61dd5]
/lib64/libc.so.6(clone+0x6d)[0x7f04c436702d]
At this point I am unsure how to proceed and so any guidance will be appreciated!
Thank you,
Ramon
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