[gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors

Mark Abraham mark.abraham at anu.edu.au
Wed Aug 11 10:20:10 CEST 2010

----- Original Message -----
From: Elio Cino <ecino at uwo.ca>
Date: Wednesday, August 11, 2010 4:33
Subject: [gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors
To: gmx-users at gromacs.org

> Hello. I have tested GBSA in 4.5 beta2 on 3 different machines: OSX 10.6 w/ core2duo, Centos5.5 w/ dual socket quad core Xenon, and another Linux machine (unsure of OS) w/ quad socket hexacore AMD Istambul. I tested the same tpr on all machines and only the core2duo runs the job successfully. The other machines give lincs errors and segmentation fault during position restrain dynamics. Normal runs (with solvent) seem fine on all machines.  I am unsure if there is a known issue with implicit solvent on certain machines so I though I would post this for testing purposes. Also, I tested the latest git with the same results. 

Just as with explicit solvent MD, if the starting configuration is a bit unhappy, then you can run into integration problems, and these will vary with things like the architecture and compiler version. Try a gentler EM-equilibration regime.


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