Re: Gradient tolerance nan for A three-atom simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 09 2009 - 16:14:33 CST

Well, what your exclude should be set to depends on your model (you said
you developed it yourself, so this is really your choice, and should be
included in your parameterization). However, if you have 1-4 or 1-3
exclusions and stretch your bonds to 10 A, the two atoms at either end
of your 3 atom system will be more than the cutoff distance apart, which
is what leads to this error... so perhaps you should use 1-2 exclusion
(which is a fairly frequent choice in CG models).
Peter

accomp lin wrote:
> 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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