Re: Gradient tolerance nan for A three-atom simulation

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Mon Jan 12 2009 - 12:03:52 CST

Hi, Peter and all:

I have a related question about exclusion:

If I got the error " Bad global exclusion error " even exclusion 1-2
is used, does it mean some of the bonds between 2 atoms are longer
than the cutoff? That would be really weird. ( I'm using CGMD with
timestep 1 fs. What's more, I got this error after 5ns' run)

Also, do you think decreasing the timestep would help in that situation?

Thanks a lot.

Bin

On Jan 8, 2009, at 11:19 AM, Peter Freddolino wrote:

> 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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