Re: simulation problems

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Mon May 14 2007 - 17:24:48 CDT

Hi there,
you should take a look at the NAMD mailing list.
A quick search on the topic of your email ended up with the following link:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2338.html

Best
Giovanni
>
> I have just started using namd so I' still learning about simulations
> and using namd.
>
>
>
> when i start simulation everything starts normally and then everything
> stops and message in log file appears:
>
>
>
>
>
> ...
>
> BRACKET: 4.72686e-007 2862.2 -1.92737e+010 -1.17053e+010 -9.76173e+009
> PRESSURE: 100 3.7681e+006 -43652 44676.8 -43652 3.80751e+006 79376.6
> 44676.8 79376.6 3.66871e+006
> GPRESSURE: 100 3.97243e+006 -32857.6 36805.4 -64533 4.01785e+006
> 96165.2 73970.8 100880 3.84696e+006
> Info: Initial time: 1 CPUs 1.65438 s/step 9.57396 days/ns 0 kB memory
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
>
>
> ENERGY: 100 143355.9983 15787.4667 247.2572
> 114.3492 -20398.7584 1181867.5228 0.0000
> 0.0000 0.0000 1320973.8358 0.0000
> 1320973.8358 1320973.8358 0.0000 3748109.5319
> 3945747.4231 86856.0000 3748109.5319 3945747.4231
>
>
>
> REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
> TCL: Running for 3000 steps
> ERROR: Constraint failure in RATTLE algorithm for atom 25!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 63!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 78!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 124!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 5!
> ERROR: Constraint failure; simulation has become unstable.
>
>
>
>
>
> appears. what is the problem??
>
>
>
>
>
> robert
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:40 CST