From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Thu Dec 24 2020 - 03:31:57 CST
Dear friend,
Use "margin 3" or larger.
-- All the best, Ashkan Shekaari, Ph.D Candidate in Solid State Physics, K. N. Toosi University of Technology, Tehran, Iran From: "Mi Yang" <drmiyang2019_at_gmail.com> To: "Bassam Haddad" <bhaddad_at_pdx.edu> Cc: "namd-l" <namd-l_at_ks.uiuc.edu> Sent: Thursday, December 24, 2020 12:14:32 PM Subject: Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). 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 < [ mailto:bhaddad_at_pdx.edu | 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 < [ mailto:drmiyang2019_at_gmail.com | drmiyang2019_at_gmail.com ] > wrote: BQ_BEGIN 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 | 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] BQ_END
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