[gmx-users] Why GROMACS is generating so many output trajectory files?

[Swapnil Wagle]

Hi..!

I am having a system with 450 Protein atoms and ~9000 water atoms. When I am 
trying to do the energy minimization step, it gives me hundreds of trajectory 
files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force 
field with TIP4P water model. The error message also says something like (one 
atom moved too far during the domain decomposition steps) which is not quite 
visible when I load the initial structure in VMD. The simulation completes 
sometimes but sometimes it also stops in the middle. Can you suggest me what 
can possibly be wrong, or any suggestion about how to remove this error?

Regards,
Swapnil Wagle
Department of Theory and Bio Systems
Max Planck Institute for Colloids and Interfaces
Potsdam-Golm, Germany D-14424
Tel.: +49-331 567-9607
Mail: swapnil.wa...@mpikg.mpg.de
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Re: [gmx-users] Why GROMACS is generating so many output trajectory files?

[Elton Carvalho]

Hello, Swapnil,

This usually means you have a problem with your topology and your
system may be in the verge of blowing up. If the simulation stops in
the middle, your system blew up.

Please read http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Regards form an unusually cloudy Natal.

On Wed, Jan 13, 2016 at 3:30 PM, Swapnil Wagle
 wrote:
> Hi..!
>
> I am having a system with 450 Protein atoms and ~9000 water atoms. When I am 
> trying to do the energy minimization step, it gives me hundreds of trajectory 
> files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force 
> field with TIP4P water model. The error message also says something like (one 
> atom moved too far during the domain decomposition steps) which is not quite 
> visible when I load the initial structure in VMD. The simulation completes 
> sometimes but sometimes it also stops in the middle. Can you suggest me what 
> can possibly be wrong, or any suggestion about how to remove this error?
>
> Regards,
> Swapnil Wagle
> Department of Theory and Bio Systems
> Max Planck Institute for Colloids and Interfaces
> Potsdam-Golm, Germany D-14424
> Tel.: +49-331 567-9607
> Mail: swapnil.wa...@mpikg.mpg.de
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> Gromacs Users mailing list
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-- 
Elton Carvalho
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