Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18).

From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Thu Dec 24 2020 - 02:44:32 CST

Dear Dr. Haddad,
a bundle of thanks. Actually the issue was with some atoms during writing
the pdb files for Ligand-protein complex.

On Tue, Dec 22, 2020 at 8:15 PM Bassam Haddad <bhaddad_at_pdx.edu> wrote:

> Hi,
>
> This is a very common error that means your system is unstable due to
> atoms moving too fast. The best way to ameliorate these issues is first, to
> interrogate the atoms in question as there could be something very
> un-physical happening. Secondly, you may want to minimize your structure,
> slowly releasing restraints over a short period of time (1 or 2 ns will be
> sufficient typically). You can also take it's suggestions, perhaps your
> 'pairlistdist' is too small, perhaps you can alter 'margin', or if you can
> get it to run long enough to produce a single restart file you can use that
> to hopefully get over the hump.
>
> Good luck.
>
> ~ Bassam
>
> On Sat, Dec 19, 2020 at 6:18 AM Mi Yang <drmiyang2019_at_gmail.com> wrote:
>
>> Please if anyone has time. Kindly comment on error:
>>
>> LDB: ============= START OF LOAD BALANCING ============== 427.397
>> LDB: ============== END OF LOAD BALANCING =============== 427.397
>> Info: useSync: 0 useProxySync: 0
>> LDB: =============== DONE WITH MIGRATION ================ 427.398
>> LDB: ============= START OF LOAD BALANCING ============== 427.472
>> LDB: Largest compute 91 load 0.012960 is 20.1% of average load 0.064504
>> LDB: Average compute 0.001270 is 2.0% of average load 0.064504
>> LDB: TIME 427.473 LOAD: AVG 0.0645037 MAX 0.0740106 PROXIES: TOTAL 268
>> MAXPE 13 MAXPATCH 7 None MEM: 3701.54 MB
>> LDB: TIME 427.473 LOAD: AVG 0.0645037 MAX 0.0740106 PROXIES: TOTAL 293
>> MAXPE 16 MAXPATCH 10 RefineTorusLB MEM: 3701.54 MB
>> LDB: TIME 427.474 LOAD: AVG 0.0645037 MAX 0.0670093 PROXIES: TOTAL 295
>> MAXPE 16 MAXPATCH 10 RefineTorusLB MEM: 3701.54 MB
>> LDB: ============== END OF LOAD BALANCING =============== 427.475
>> Info: useSync: 0 useProxySync: 0
>> LDB: =============== DONE WITH MIGRATION ================ 427.476
>> ERROR: Atom 22221 velocity is -14189.9 27.0305 6562.5 (limit is 10000,
>> atom 777 of 999 on patch 42 pe 18)
>> ERROR: Atom 4063 velocity is 17381.5 -1472.13 -10044 (limit is 10000,
>> atom 997 of 999 on patch 42 pe 18)
>> ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
>> patch 42 pe 18).
>> FATAL ERROR: Low global exclusion count! (89972 vs 89977) System
>> unstable or pairlistdist or cutoff too small.
>>
>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>> [0] Stack Traceback:
>> [0:0] [0x20094910]
>> [0:1] [0x204abb66]
>> [0:2] [0x204b3616]
>> [0:3] [0x204a1a42]
>> [0:4] [0x20c01e60]
>> [0:5] [0x21132c80]
>>
>>

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