[gmx-users] SWM4_DP water on graphite surface

[Mark Abraham]

On 28/04/2012 10:54 AM, Ho, Tuan A. wrote:
>
> Thank Mark,
>
> I freeze the SOL because I would like to check if it is because of SOL 
> bad contact.
>

You can't do a dynamical simulation with zero degrees of freedom.

> However, it turns out that the graphite deformation is the problem.
>

Under what conditions? Your earlier simulation probably blew up because 
of the above.

Mark

> My friend asks me to use only one processor, and it is running well 
> (no SOL freeze). Hopefully, after I got the final configuration for 
> serial run, I will be able to perform a parallel simulation.
>
> Thank you so much.
>
> Any idea for this problem is highly appreciated since I am not sure if 
> I will be able to perform a parallel job.
>
> Tuan.
>
> *From:*gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Mark Abraham
> *Sent:* Friday, April 27, 2012 6:36 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] SWM4_DP water on graphite surface
>
> On 28/04/2012 3:33 AM, Ho, Tuan A. wrote:
>
> Dear Gromacs users,
>
> I would like to simulate a thin film of SWM4_DP water on graphite 
> surface. First, I equilibrate the water only (run very well), then I 
> add a graphite surface on it. I freeze the graphite surface but the 
> graphite surface acted crazily after a few time step (graphite surface 
> deform critically, "blow"). The error is
>
> Step 140:
>
> The charge group starting at atom 266 moved than the distance allowed 
> by the domain decomposition (1.000000) in direction Z
>
> distance out of cell 1.038218
>
> Old coordinates:    0.123    2.627    6.000
>
> New coordinates:    0.013    0.671   11.038
>
> Old cell boundaries in direction Z:    5.978   10.000
>
> New cell boundaries in direction Z:    5.660   10.000
>
> -------------------------------------------------------
>
> Program mdrun, VERSION 4.0.7
>
> Source code file: domdec.c, line: 3654
>
> Fatal error:
>
> A charge group moved too far between two domain decomposition steps
>
> This usually means that your system is not well equilibrated
>
> I don't understand why I freeze the graphite surface but the carbon 
> atom moved around. If it is because of bad contact, I think the water 
> should be blown instead of carbon atom
>
> I ran the SPC/E water model on graphite very well.
>
>
> Probably you didn't use freezedim on the SOL degrees of freedom when 
> you used that water model, as you have here.
>
> Mark
>
>
> I attached the mdp file, the topology file.
>
> Please let me know if I did anything wrong.
>
> Thanks in advance.
>
> Tuan.
>
>
>
>
>

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