[gmx-users] Problems of gmx4.5.5 on the E3-1230 V2 CPU (Ivy Bridge)

[石子枫]

Dear，every one!

We found some problems of run gmx4.5.5 in parallel on the E3-1230 V2 CPU (Ivy Bridge).
The compilers we used were ifort and icc (Version 12.0.3).
It only if the value of the option "-nt" > 2, the mdrun program crashed after hundreds MD steps.
And we also noticed that the same .tpr file could successfully run on both the i7-2600 and AMD platforms.

The typically error outputs are attached below. Thanks for any responses and suggestions.

Wade Lv


Error Outputs:
==================================================
step 222: Water molecule starting at atom 3633 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 222: Water molecule starting at atom 3882 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
=====================================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120525/79256599/attachment.html>