[gmx-users] SWM4_DP water on graphite surface

[Ho, Tuan A.]

Thank Mark,
I did not freeze the SOL. My graphite surface blew up. The system is: A water film is about 6A from graphite surface. The water film is equilibrated before placed on graphite surface.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Friday, April 27, 2012 8:02 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SWM4_DP water on graphite surface

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> [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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