Re: Error NPT simulation - Need Urgent Help - Reg

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Fri Aug 31 2018 - 08:38:44 CDT

Dear all,

                 After increasing margin also I am getting the same error.
Is there any way to resolve these issue.

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: Low global exclusion count! (2337723 vs 2337729) System
unstable or pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Regards,

MANIKANDAN D

On Wed, Aug 29, 2018 at 10:20 PM Radak, Brian K <bradak_at_illinois.edu> wrote:

> Please send general use questions to the namd-l list only (not namd)
>
> This is a well-established occurrence in NAMD and there are several, if
> not dozens, of posts on this list regarding the problem and solution.
>
> Your density does not appear to be well equilibrated and, as a result, the
> box is changing volume too quickly for the domain decomposition to keep up.
> You can:
>
> 1) choose a better starting density
> 2) choose a larger margin (this may hurt performance, so use the default
> once equilibration is achieved)
> 3) run shorter NpT segments so that the patches are re-allocated more
> frequently
>
> For very small and very diffuse systems, none of these may work.
>
> Brian Radak
> Postdoctoral Associate, Software Development
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> bradak_at_ks.uiuc.edu
> ------------------------------
> *From:* Mani Kandan [manikandand5110_at_gmail.com]
> *Sent:* Wednesday, August 29, 2018 12:35 PM
> *To:* namd-l_at_ks.uiuc.edu; namd_at_ks.uiuc.edu
> *Subject:* Error NPT simulation - Need Urgent Help - Reg
>
> 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
>
>
> Regards,
>
> MANIKANDAN D
>

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