[gmx-users] LINCS

[Neda Rafiee]

Thanks Joao. My problem was solved after I changed mdrun options. 


----- Original Message -----
From: "João Henriques" <joao.m.a.henriques at gmail.com>
To: gmx-users at gromacs.org
Sent: Sunday, April 9, 2017 4:44:22 PM
Subject: Re: [gmx-users] LINCS

Dear Neda,

I'm not sure I appreciate the ellipses after "thanks". After all, I took
some of my personal time - on a Sunday - to do your work and Google search
for the key words in your error message. Plus, I sent you the link and
pointed you to the right section, which contains a crystal clear
explanation of some of possible reasons for this error.

In any case, to avoid having someone think I am being purposely
condescending, I will tell you that your system cannot be decomposed into
the requested 16 MPI ranks. This is likely due to the fact that it is too
small and decomposing the simulation box into 16 parts would break one or
more of the following things: (i) the size of the largest charge group or
bonded interaction, (ii) the largest of rvdw, rlist and rcoulomb, or (iii)
other parameters associated with bond constraints. You need to experiment
using a lower number of MPI ranks. Then again, without any information
about your system, Gromacs version, etc, it is impossible to pinpoint the
exact reason.

Best regards,
/J

On Sun, Apr 9, 2017 at 1:38 PM, Neda Rafiee <nerafiee at ipm.ir> wrote:

> Thanks....
>
> ----- Original Message -----
> From: "João Henriques" <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Sent: Sunday, April 9, 2017 3:37:46 PM
> Subject: Re: [gmx-users] LINCS
>
> Google is your friend, *always*.
>
> Please see the last section on:
>
> http://www.gromacs.org/Documentation/Errors
>
> /J
>
> On Sun, Apr 9, 2017 at 10:00 AM, Neda Rafiee <nerafiee at ipm.ir> wrote:
>
> > Dear gmx-users,
> > I have a problem in doing nv pequilibration for my pritein-water system,
> I
> > do not understand the error:
> > There is no domain decomposition for 16 ranks that is compatible with the
> > given box and a minimu$
> > Change the number of ranks or mdrun option -rcon or -dds or your LINCS
> > settings
> > Look in the log file for details on the domain decomposition
> >
> >
> >
> > --
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