Re: Gradient tolerance nan for A three-atom simulation

From: accomp lin (accomplin_at_yahoo.com.cn)
Date: Fri Jan 09 2009 - 02:51:43 CST

Hi  Gumbart

My exclusion is set to scaled1-4 and the bond of my system is about 5 A. I'm going to stretch them to 10 A. So then I should set the exclusion to NONE? or other values? And what is patch in NAMD? I've heard it a lot but I have no clue of what is it or how does it work. Thanks

regards

Jiaqi

--- 09年1月9日,周五, Peter Freddolino <petefred_at_ks.uiuc.edu> 写道:
发件人: Peter Freddolino <petefred_at_ks.uiuc.edu>
主题: Re: namd-l: Gradient tolerance nan for A three-atom simulation
收件人: accomplin_at_yahoo.com.cn
抄送: "JC Gumbart" <gumbart_at_ks.uiuc.edu>, namd-l_at_ks.uiuc.edu
日期: 2009,19,周五,3:19上午

Hi Jiaqi,
it is important to understand the source of the bad global exclusion
count error: Two atoms which should have an exclusion are not on
neighboring patches. This happens a lot in coarse grained systems
because they have such long bonds. What do you have exclude set to? And
how far apart are your particles?
Peter

accomp lin wrote:
> Hi Gumbart
>
> Thanks very much for your help.The problem had been solved when I
> altered the angle a little from 180.(My theta0 is also 180 degree).
>
> However , I got another error , it said:
>
> Reason: FATAL ERROR: Bad global exclusion count!
>
> The problem occurs at different time step with different set of
> initial coordinates of the atoms. I then I changed the cutoff ,
> switchdist, and pairlistdist to be very little and set the parameter
> of LJ potential zore, the simulation ran successfully. But when I set
> the cutoff, swithdist and pairlistdist to be normal, the error came
> back again. Wht does these parameter matter, since the LJ potential is
> already zore? How come it to be a problem in my three-atoms system?
>
> Thanks, best.
>
> Jiaqi.
>
>
> --- *09年1月6日,周二, JC Gumbart /<gumbart_at_ks.uiuc.edu>/*
写道:
>
> 发件人: JC Gumbart <gumbart_at_ks.uiuc.edu>
> 主题: RE: namd-l: Gradient tolerance nan for A three-atom simulation
> 收件人: accomplin_at_yahoo.com.cn, namd-l_at_ks.uiuc.edu
> 日期: 2009,16,周二,1:24下午
>
> I wonder if this happens because theta=180 is an indeterminate
> problem? What if you try offsetting the third atom from the line
> of the other two? What is the theta0 you’ve set in the parameter
> file?
>
>
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> *On Behalf Of *accomp lin
> *Sent:* Monday, January 05, 2009 11:10 PM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: Gradient tolerance nan for A three-atom simulation
>
>
>
> Dear NAMD developer:
>
>
>
> I've modifed a namd source code with New bond energy
> potentials for my Coarse Grained models. After I recompiled it
> successfully on linux, I constructed a three-atom model to test my
> new NAMD. Only bond and angle are included in the psf file, the
> three atoms are aligned straight, each of them have a mass of 400
> amu. But when I run the program, the simulation held still and had
> the following error.
>
>
>
> /INITIAL STEP: 1e-06 //
> /GRADIENT TOLERANCE: nan //
> /BRACKET: 0 0 nan nan nan// /
>
>
>
> After several try and visiting the Mailing list I found I was the
> Angle term tha caused the problem. When I turned it off or set the
> /Ktheta /zore the problem dissappeared. I already set a large
> enough boundry box the contain all the atoms within it. I know it
> might be a little inappropriate to use NAMD do to such a simple
> simulation, for it can cause various problems. But I really want
> to know how does it work and how to solve these problems. So
> please help, thank you.
>
>
>
>
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