GROMACS development

01/16/2014

08:12 PM GROMACS Bug #1166: g_order is incorrect for unsaturated carbons

I encountered the bug that Chris refers to here and wanted to chime in on its origin in the existing g_order code. Th...

06/09/2013

04:14 PM GROMACS Feature #1168: g_density does not do what users think it does, given PBC over z and constant pressure simulation

I'd like to add two more small issues in g_density that I think might want to be clarified or changed and thought thi...

05/22/2013

12:30 AM GROMACS Bug #1262 (Closed): g_select documentation error

I found a small error in the g_select documentation. One of the examples is:
All atoms farther than 1 nm of a fixe...

03/10/2013

05:48 PM GROMACS Bug #1184: Affinity setting failed bug

Sorry and just to be clear the output of the printf statements was the same independent of whether pinning was on (as...

05:47 PM GROMACS Bug #1184: Affinity setting failed bug

Hi Roland,
I think these processors lack hyper-threading (http://ark.intel.com/products/33081/Intel-Xeon-Processor...

04:30 PM GROMACS Bug #1184: Affinity setting failed bug

A few updates from me:
Using same hardware/software info as in my initial post (i.e. I did not update my Kernel), ...

03/07/2013

09:02 PM GROMACS Bug #1184 (Closed): Affinity setting failed bug

I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to v 4.6. I'm using older 8 core Intel Xeon E...

01/09/2013

05:03 PM GROMACS Bug #1109: gmxcheck and GROMOS 96 bonds

I implemented the change exactly as Justin suggested above and it works correctly. If only they were all this easy, r...

01/08/2013

05:36 PM GROMACS Bug #1109 (Closed): gmxcheck and GROMOS 96 bonds

I was using gmxcheck to check a simple trajectory of surfactants, and get many errors of the type "Distance between a...