MAINLOOP: overlap in initial configuration
Brought to you by:
marcus_martin
Menu
▾
▴
#6 MAINLOOP: overlap in initial configuration
I have a periodic polymer system that I've successfully run NVT MD using lammps and had absolutely no problems. When I use the same system in Towhee for a simple NVT simulation using the same forcefield, Towhee terminates with an error message: MAINLOOP: overlap in initial configuration
I know that there are no spatially-close contacts in the system. What is actually wrong and how can we get Towhee to cooperate?
Seems most likely something is going wrong in the scripts that turn the input from LAMMPS into Towhee. Those rarely get tested and most still date back to when LAMMPS was written in FORTRAN. If you send me the relevant LAMMPS and Towhee files I can take a look to try and sort out what is happening.
My first instinct is it probably is related to something going wrong with the coordinate frames for a molecule that wraps through the simulation box in complicated ways. If that is the case, then it should be relatively easy to sort out that logic for this case and get a bug fix released.
Marcus
marcus_martin@users.sf.net
Hi Marcus,
Thanks so much for taking a look at this. It's been many years since I've used Towhee, but I'm happy to get back to this wonderful tool!
I'm using the MAPS interface, so I'm sending you all the relevant files. The attached is a gzip'ed tar file. I've removed the MIME suffice to get through the mail.
Sincerely,
Steve
~~~~/)~~~/)~~~/)~~~/)~~~~
Steve Lustig, Ph.D.
Associate Professor
Associate Chair for Research
Department of Chemical Engineering
Northeastern University
http://www.che.neu.edu/people/lustig-steve
From: Marcus Martin marcus_martin@users.sourceforge.net
Sent: Monday, April 1, 2019 4:02 PM
To: [towhee:support-requests]
Subject: [towhee:support-requests] #6 MAINLOOP: overlap in initial configuration
Seems most likely something is going wrong in the scripts that turn the input from LAMMPS into Towhee. Those rarely get tested and most still date back to when LAMMPS was written in FORTRAN. If you send me the relevant LAMMPS and Towhee files I can take a look to try and sort out what is happening.
My first instinct is it probably is related to something going wrong with the coordinate frames for a molecule that wraps through the simulation box in complicated ways. If that is the case, then it should be relatively easy to sort out that logic for this case and get a bug fix released.
Marcus
marcus_martin@users.sf.net
[support-requests:#6]https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Ftowhee%2Fsupport-requests%2F6%2F&data=02%7C01%7Cs.lustig%40northeastern.edu%7C9b2258c3000a4a295de708d6b6dcf3bf%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C1%7C636897457446115950&sdata=JCZScy%2FPpgVqu9vKd%2Fnvg2BqJsaUq1z9Nq5Gw9XmVpY%3D&reserved=0 MAINLOOP: overlap in initial configuration
Status: open
Group: v1.0_(example)
Created: Mon Apr 01, 2019 07:38 PM UTC by Steve Lustig
Last Updated: Mon Apr 01, 2019 07:38 PM UTC
Owner: nobody
I have a periodic polymer system that I've successfully run NVT MD using lammps and had absolutely no problems. When I use the same system in Towhee for a simple NVT simulation using the same forcefield, Towhee terminates with an error message: MAINLOOP: overlap in initial configuration
I know that there are no spatially-close contacts in the system. What is actually wrong and how can we get Towhee to cooperate?
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/towhee/support-requests/6/https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Ftowhee%2Fsupport-requests%2F6%2F&data=02%7C01%7Cs.lustig%40northeastern.edu%7C9b2258c3000a4a295de708d6b6dcf3bf%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C1%7C636897457446125958&sdata=iFxbo0Z69uSlWQ1pKM2j5Ccy4ePpU91o9jFqyY%2F3ZAA%3D&reserved=0
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fauth%2Fsubscriptions%2F&data=02%7C01%7Cs.lustig%40northeastern.edu%7C9b2258c3000a4a295de708d6b6dcf3bf%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C1%7C636897457446135965&sdata=xftNTzb0GNg9gjt6YpwdexIqgycghn98Lp6wt6F3PXM%3D&reserved=0
Related
Support Requests: #6
Sorting through the files trying to figure out what is going wrong. Since I am not sure what the simulation is supposed to look like I need to ask some questions when I hit parts I think are strange to see if that is a problem, or a deliberate choice.
The hmtraix values are unusual in your input file.
hmatrix
37.2315 0 0
0.311405 65.2839 0
-6.37732 -12.9964 13.8888
Is this intentional? A "normal" brick-shaped box woud just have terms on the diagonals and the third line of this hmatrix is very unusual.
Marcus