Archive from user: Ramon Guixa-Gonzalez Systems become extremely unstable (i.e. very large box fluctuations) after 80-100 ns until they eventually deform (i.e. membrane abnormally enlarged, big water pores go through, and protein collapses). None of the following actions helps: 1 - Increase/decrease certain parameters within the mdp file (e.g. tau- 2 - Re-build and re-equilibrate the system. 3 - Use of different GROMACS versions, namely 5.4, gromacs2016 and gromacs2018. 4 - Use of different computers and different GPUs models. 5 - Use of a different system (other membrane proteins of the same family with different ligands). Sooner or later, same thing happens over and over again in every protein-membrane system. Intriguingly, systems never crash (i.e. simulations keep on running despite of the observed artifacts). Thus, the gromacs+CHARMM36+GPUs combination inevitably induces protein-membrane systems to collapse. The only workaround so far is running the system using only CPUs. *(from redmine: issue id 2845, created on 2019-01-28 by gmxdefault, closed on 2019-09-24)* * Relations: * relates #2867 * Changesets: * Revision 4576f802ac81b07a49c7c4ad21d3bf15831979a7 by Berk Hess on 2019-02-01T14:53:11Z: ``` Fix incorrect LJ repulsion force switching on GPUs When using a CUDA or OpenCL GPU, the coefficient for the second order term for the LJ repulsion in the force (not energy) switching function, called 'A' in the manual, had the wrong sign in both the force-only kernels and the force+energy kernels. Note that the dispersion force switching was correct. Fixes #2845 Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748 ``` * Revision de27733a387922033b116bf7024c595e5b1e99a8 by Berk Hess on 2019-02-04T13:26:07Z: ``` Fix incorrect LJ repulsion force switching on GPUs When using a CUDA or OpenCL GPU, the coefficient for the second order term for the LJ repulsion in the force (not energy) switching function, called 'A' in the manual, had the wrong sign in both the force-only kernels and the force+energy kernels. Note that the dispersion force switching was correct. Cherry-picked from 2019 Fixes #2845 Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748 ``` * Revision c131d790b48da10f5fcb9e4aabeef0d730b76724 by Berk Hess on 2019-02-20T07:59:12Z: ``` Fix incorrect LJ repulsion force switching on GPUs When using a CUDA or OpenCL GPU, the coefficient for the second order term for the LJ repulsion in the force (not energy) switching function, called 'A' in the manual, had the wrong sign in both the force-only kernels and the force+energy kernels. Note that the dispersion force switching was correct. Cherry picked from 2019 Fixes #2845 Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748 ``` * Revision 8fc3cc55a0a0721fc9c336f142a33025d18b4d5f by Berk Hess on 2019-09-21T10:01:55Z: ``` Fix incorrect shift forces for CMAP The shift force indices were inverted for the second and third atom in the CMAP term, leading to incorrect virial and pressure contributions when these atoms resided in different periodic images. Fixes #2845 and #2867 Change-Id: I1946a1d375d6c62e4e6d23ee25b92b42a3d4a6f7 ``` * Revision 771d4c99c5aca3ac2e1b4892417898b6686d045a by Berk Hess on 2019-09-21T10:37:04Z: ``` Fix incorrect shift forces for CMAP The shift force indices were inverted for the second and third atom in the CMAP term, leading to incorrect virial and pressure contributions when these atoms resided in different periodic images. Fixes #2845 and #2867 Also prepares branch for another point release. Change-Id: I1946a1d375d6c62e4e6d23ee25b92b42a3d4a6f7 ``` * Uploads: * [bug.zip](/uploads/c9edaaedbc39565c79c5e6225ce8be64/bug.zip) * [simfiles.zip](/uploads/4e79c874ad5a3d0eaf34dc6b5548466c/simfiles.zip) * [logConcat](/uploads/091d9916bd4c2c8b68881fa53dd09771/logConcat) * [2016_6.zip](/uploads/bcc115ca9c8ca9c9d9eff6e2b035e296/2016_6.zip) *  *  *  *  * [run1Concat.log](/uploads/edb2cdfffbd8011a3be6ad45abcd81f6/run1Concat.log) * [plainCutoff.zip](/uploads/abae740a44811ce8d7bfb3dc01d93fea/plainCutoff.zip) * [runLog](/uploads/c9f935a3712d11718eeab6c937157dc6/runLog) * [bug0.zip](/uploads/a2f7b7ef6ac15a8b72a0719e0c078289/bug0.zip) * [bug1.zip](/uploads/a309c1db4f425f030a5c1c0b43e25d8b/bug1.zip) * [newSys0.zip](/uploads/a5bacf1e1ab6a2d66c90b32c9b99f73d/newSys0.zip) * [newSys1.zip](/uploads/d55f5b2ebcb8b8072e0f87be15d10e0f/newSys1.zip) *  * [repro_bug.tar.gz](/uploads/614564306c524bea5c39b371c5e1249d/repro_bug.tar.gz) * [state_save0.cpt](/uploads/b5210ba54d4963f9106bab0519524974/state_save0.cpt) * [compare.pdf](/uploads/02339df8dbc023b559e247e521396e58/compare.pdf) *  *