Re: Error NPT simulation - Need Urgent Help - Reg

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Aug 29 2018 - 12:01:46 CDT

Dear Manikandan,

The error you see can result from the periodic cell size getting compressed in response to the barostat, so that for the initial spatial decomposition of atoms into patches, the length of a given patch becomes too small for the choice of cutoff, pairlist distance, and hydrogen group size. One approach is to increase the patch "margin" value until your system is better equilibrated.

Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On Aug 29, 2018, at 11:35 AM, Mani Kandan <manikandand5110_at_gmail.com> wrote:
> 
> Dear all,
>                       I am getting the following error while running NPT simulation. I am running NPT after minimization, but in minimization, there is no problem. NPT is running for 60 steps and showing this error. The same code runs very well when system dimensions of 100 A. Kindly help me in this regard.
>                       
> 
> 
> The last position output (seq=60) takes 0.198 seconds, 535.676 MB of memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 60
> FINISHED WRITING RESTART VELOCITIES
> ERROR: Margin is too small for 25467 atoms during timestep 67.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> FATAL ERROR: High global exclusion count!  (1282894 vs 868383)  System unstable or pairlistdist or cutoff too close to periodic cell size.
> 
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html <http://www.ks.uiuc.edu/Research/namd/bugreport.html>
> 
> 
> Regards,
> 
> MANIKANDAN D

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