Re: Query for coarse grain system

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 05 2018 - 10:17:47 CDT

This is squarely a NAMD question: removing vmd-l.

The CUDA compute kernels were significantly modified multiple times in the
past versions. Without stating which versions you used, you are not really
asking a question that can be answered.

Also, have you looked at the trajectory before the error shows up? Well,
this *will* involve VMD but there should be no question involved, since it
should be standard practice to monitor the progress of the simulation.

Giacomo

On Thu, Apr 5, 2018 at 10:53 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
wrote:

> Hi,
>
>
> i am working on graphene-lipid system for coarse grain MD and I have
> encountered a strange problem (might be i don't understand it correctly). i
> need your suggestions to understand what is causing warning.
>
> During MD, when I run a system on CUDA based GPU (+p32; 4 GPU) system I
> encounter following error:
>
> Warning: Low global CUDA exclusion count! (6547 vs 6552) System unstable
> or pairlistdist or cutoff too small.
>
> i understand it is due to the reasons explained here
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.
> 2013-2014/3253.html, http://www.ks.uiuc.edu/Researc
> h/namd/mailing_list/namd-l.2009-2010/2786.html
> and here http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.
> 2010-2011/3814.html
>
> Although, when I run this same system on my linux PC I don't observe this
> error (+p8 1 GPU) and MD runs smoothly without any error or warning.
>
> Can any one please explain what I am missing here or what is potential
> problem I need to fix.
>
>
> Thanks in advance
>
> Abhi
>
>
> Abhishek Tyagi, PhD
>
> Chemical and Biological Engineering
>
> Hong Kong University of Science and Technology
>
> Clear Water Bay, Hong Kong
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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