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Feature #1192

Add support for Verlet scheme with Buckingham

Added by Bu Wang about 4 years ago. Updated 8 months ago.

Status:
Accepted
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Difficulty:
uncategorized
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Description

We are trying to simulate a simple alumina crystal. The forcefield only contains non-bonded interactions defined with our own Buckingham potentials. Everything works fine with the group cutoff scheme. But with the similar settings in Verlet scheme, the simulation would blow up right after step 0 with a segmentation fault error. GDB shows the error happens in pme.c: 415 idxptr[ZZ] = pme->nnz[tiz]. Taking the group scheme .tpr and run mdrun -testverlet fails in the same way.

The step 0 information shows absurdly high buckingham energy and kinetic energy. We tried modifying parameters related to the Verlet scheme, such as verlet-buffer-drift, vdw-modifier and rvdw-switch, but had no luck. We also compared the outputs from group and Verlet schemes but couldn't see anything weird.

I attached the .mdp; changing the cutoff-scheme to group and setting rlist=1.2 will make the simulation run. The .tpr and topology are also attached.

I would greatly appreciate any suggestions. Thanks in advance!

6x7x1.mdp (11 KB) Bu Wang, 03/16/2013 03:43 AM

6x7x1.tpr (175 KB) Bu Wang, 03/16/2013 03:43 AM

6x7x1.top (1.6 KB) Bu Wang, 03/16/2013 03:43 AM


Related issues

Related to GROMACS - Feature #1347: future of tables New

Associated revisions

Revision 81b1cd9b (diff)
Added by Rossen Apostolov almost 3 years ago

Added a note about unsupported Verlet cutoff + Buckingham.

Refs #1192.

Change-Id: I2da3bf8c768de40531e1ffdf6f8cec73c9e53314

History

#1 Updated by Berk Hess about 4 years ago

  • Status changed from New to In Progress
  • Assignee set to Berk Hess
  • Target version changed from 4.6.1 to 4.6.2
  • Affected version - extra info set to 4.6.1

#2 Updated by Mark Abraham almost 4 years ago

  • Target version changed from 4.6.2 to 4.6.3
  • Affected version set to 4.6.3

#3 Updated by Mark Abraham over 3 years ago

  • Target version changed from 4.6.3 to 4.6.x

#4 Updated by Szilárd Páll over 3 years ago

This has been marked as "in progress" for quite a long time. Has the issue been identified? Is the status still valid or should we set it to "Accepted"?

#5 Updated by Bu Wang over 3 years ago

The issue was that Buckingham or tabulated potentials were not supported by the verlet cutoff scheme. Is there a plan to add the support in a future version?

#6 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1192.
Uploader: Rossen Apostolov ()
Change-Id: I2da3bf8c768de40531e1ffdf6f8cec73c9e53314
Gerrit URL: https://gerrit.gromacs.org/3440

#7 Updated by Rossen Apostolov almost 3 years ago

  • Status changed from In Progress to Fix uploaded

#8 Updated by Rossen Apostolov almost 3 years ago

  • Tracker changed from Bug to Feature
  • Subject changed from Segmentation fault switching from group to verlet cutoff shceme to Add support for Verlet scheme with Buckingham
  • Status changed from Fix uploaded to Accepted
  • Priority changed from High to Normal

Changed the report to a "feature"

#9 Updated by Mark Abraham almost 3 years ago

  • Target version changed from 4.6.x to 5.x

There are plans to support tabulated potentials with the Verlet scheme and GPUs, perhaps in 5.1. Native Buckingham kernels would only be considered after we produce a Verlet kernel generator sometime this year; perhaps it might be straightforward at that time.

#10 Updated by Berk Hess almost 3 years ago

But we should put a proper fatal error in 4.6 and 5.0, right?

#11 Updated by Mark Abraham almost 3 years ago

I think Rossen's patch does an OK job. Could also fatal in grompp.

#12 Updated by Mark Abraham over 1 year ago

#13 Updated by Mark Abraham 8 months ago

  • Target version deleted (5.x)

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