[gmx-users] SWM4_DP water on graphite surface
Ho, Tuan A.
tuanho at ou.edu
Sat Apr 28 02:54:51 CEST 2012
I freeze the SOL because I would like to check if it is because of SOL bad contact. However, it turns out that the graphite deformation is the problem.
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.
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
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
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.
I attached the mdp file, the topology file.
Please let me know if I did anything wrong.
Thanks in advance.
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