[gmx-users] error in a parallel job

[David]

On Sat, 2003-11-15 at 04:14, Lanyuan Lu wrote:
> A micelle in CO2. The only particular feature I can think about is that
> I used dummy atoms to produce the linear rigid model of CO2. Can
> this be a reason? I guess when the gromacs devided the box into 2,
> it broke some bonds. maybe that's the reason I got the error for
> SHAKE. The input file is like:
> [ moleculetype ]
> ; Name   nrexcl
> CO2      3
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr        charge          mass
>      1      CO       1     CO2        CO     1          0.6512
>      2      OO       1     CO2        OO     1        - 0.3256
>      3      OO       1     CO2        OO     1        - 0.3256
>      4      RM       1     CO2        RM     1          0.0
>      5      RM       1     CO2        RM     1          0.0
> [dummies2]
> 1    4    5    1    0.5
> 2    4    5    1    -0.0862
> 3    4    5    1    1.0862
> [ constraints ]
> 4    5    1    0.196
> [exclusions]
> 1 2 3 4 5
> 2 1 3 4 5
> 3 1 2 4 5
> I calculated the same micelle with single point CO2 model without problem.
> But for this 3-site CO2, It breaks often.

I don't see anything wrong with the topology off hand. You can make
testing a bit easier by first trying a small box with only CO2 (an odd
number of molecules!). If that crashes as well on two processors, you
may send me your input files and I'll have a look.

> Thanks.
> Lanyuan Lu
> 
> ----- Original Message ----- 
> From: "David" <spoel at xray.bmc.uu.se>
> To: <gmx-users at gromacs.org>
> Sent: Friday, November 14, 2003 2:30 PM
> Subject: Re: [gmx-users] error in a parallel job
> 
> 
> > On Fri, 2003-11-14 at 20:24, lulanyuan wrote:
> > > In short. For a certain system A I can calculate it using 1 processor but can not using 2. For other systems I can use any
> > > number of processors (1,2,4 etc) as I like. So what's the problem about system A? 
> > > The error message I got was shake didn't converge. I din't change any condition other than number of processors.
> > > Thanks.
> > > Lanyuan
> > 
> > either your starting conformation or something peculiar about system A.
> > so what is system A?
> > 
> > > >Hello, everyone. I got a strange problem when I simulated
> > > >a system using two processors. The job is ok with one processor.
> > > >But when I try to calculate it using two, I got it broken in
> > > >the middle. In the log file I found a lot of error message saying shake was not converged in 1000 steps.
> > > >For other simulations, I got no problem for parallel jobs.
> > > >Can anyone give me a clue?
> > > >not without more information.
> > > 
> > > >Thank you very much.
> > > >Lanyuan Lu
> > > ______________________________________
> > > ===================================================================
> > > °®¹úÕßÊýÂëÏà»ú°éÂÂÍõ--´øÉÏ555¸ö½º¾íÈ¥ÂÃÓÎ (http://ad4.sina.com.cn/shc/zhuiyu_hprefresh.html)
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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