From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Dec 02 2020 - 19:35:52 CST
Constraints/restraints can play poorly with pressure control... you may
need to tone them down or use a shorter timestep until the system volume
stabilizes. Are you running a constant pressure simulation?
Best,
Peter
On Wed, Dec 2, 2020 at 8:24 PM Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
wrote:
> I think the termination was occurring due to the simulation taking up too
> much memory and I seem to have fixed this by increasing restartfreq and
> dcdfreq. After, fixing this I get the error that I was initially trying to
> fix:
>
> ERROR: Constraint failure in RATTLE algorithm for atom XXXX!
> ERROR: Constraint failure; simulation has become unstable.
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
> *Sent:* Wednesday, December 2, 2020 12:43 PM
> *To:* NAMD Listserve <namd-l_at_ks.uiuc.edu>
> *Subject:* namd-l: Termination between Minimization to Equilibration
>
> 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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