Re: Query for coarse grain system

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Thu Apr 05 2018 - 10:23:18 CDT

Dear Giacomo,

Thanks for the reply.

I am using namd 2.11 version. i have looked at the trajectories and they seems normal to me, for the CUDA-GPU the warning is coming still md is running similar to md on PC.

Thanks

Abhi

Abhishek Tyagi,PhD

Chemical and Biological Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Thursday, April 5, 2018 11:17:47 PM
To: NAMD list; Abhishek TYAGI
Subject: Re: namd-l: Query for coarse grain system

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<mailto: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/Research/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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