From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Thu Sep 10 2020 - 04:35:27 CDT
Thank you very much Natalia,
Does you mean setup the constrain parameters as:
constraintScaling {10, 5, 2, 1, 0.5, 0.1}
or separate them in six time rounds?
Zhihong Xin
发件人：Natalia Ostrowska <n.ostrowska_at_cent.uw.edu.pl>
发送日期：2020-09-10 16:40:27
收件人：namd-l_at_ks.uiuc.edu,"辛志宏" <xzhfood_at_njau.edu.cn>
主题：Re: namd-l: ERROR: Atoms moving too fast; simulation has become unstable
There should probably be something between those two lines:
minimize 100
run 2000
I am running non-QM simulations, so there could be other problems too, but I suggest adding water thermalization and equilibration steps. So, first you freeze the molecule or semi-freeze with constraints and gradually increase the temperature eg from 10 to 310 and then gradually decrease the harmonic constraints for your molecule, I am doing it for a list of k values {10, 5, 2, 1, 0.5, 0.1}, with like 10 ps for each step or more. And minimise for 1000 steps instead of 100.
Regards,
Natalia Ostrowska
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory
czw., 10 wrz 2020 o 06:05 辛志宏 <xzhfood_at_njau.edu.cn> napisał(a):
Dear all,
I am running a QM/MM in a minimization simulation and come across an error as follows, I searched the namd mailing list and re-setup the "cellOrigin" parameter by PBC box, however, the issue still not solved, how to fix the issue? Any suggestion will be much appreciated.
the constrain parameter
# mobile atom selection:
constraints on
consexp 2
consref YZZ-restraint.pdb
conskfile YZZ-restraint.pdb
conskcol B
constraintScaling 2.0 #(when the value set to 5, an error will occured )
the minization parameter
# Number of steps in the QM/MM simulation.
minimize 100
run 2000
the error information,
............................
ERROR: Atom 1450 velocity is 44316.2 -3353.86 6839.1 (limit is 24000, atom 353 of 1140 on patch 12 pe 2)
ERROR: Atom 1452 velocity is -45752.6 3605.38 -6493.9 (limit is 24000, atom 355 of 1140 on patch 12 pe 2)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 12 pe 2).
WRITING COORDINATES TO DCD FILE YZZ-QM-min-out.dcd AT STEP 106
PRESSURE: 106 3.31643e+07 -558377 1.32687e+06 -1.12782e+06 3.0385e+07 -219407 567553 -178116 2.87595e+07
GPRESSURE: 106 2.94489e+07 -265347 697993 -825602 3.01241e+07 -211842 63017.7 -129475 2.83545e+07
TIMING: 106 CPU: 39.6919, 0.710148/step Wall: 43196, 1051.59/step, 582.464 hours remaining, 1200.250000 MB of memory in use.
ENERGY: 106 312845.5932 85634.6330 2984.7089 556.0897 -117499.8095 11452066.5021 23532359.8716 -2151894.5182 6038397.7682 39155450.8389 68833.6161 33117053.0707 37421208.5062 68833.6161 30769621.5966 29309160.5714 91937.0412 30769621.5966 29309160.5714
FATAL ERROR: Exiting prematurely; see error messages above.
Zhi hong Xin
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:14 CST