[gmx-users] error in a parallel job
lulanyuan at sina.com
Sat Nov 15 04:16:01 CET 2003
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
[ 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
1 4 5 1 0.5
2 4 5 1 -0.0862
3 4 5 1 1.0862
[ constraints ]
4 5 1 0.196
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.
----- 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
> > ______________________________________
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> 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
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