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-boun...@gromacs.org
[mailto:gmx-users-boun...@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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