[gmx-users] Energy minimizations taking really, really long?

I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps.

Re: [gmx-users] 'Command not found' after installation

That worked! Thanks a ton! From: Justin Lemkul To: Nimmy McNimmerson ; Discussion list for GROMACS users Sent: Sunday, August 25, 2013 2:54 PM Subject: Re: [gmx-users] 'Command not found' after installation On 8/25/13 5:31 PM, Nimmy McNimme

Re: [gmx-users] 'Command not found' after installation

enforces dynamic linking, go figure!), * when you're really sure you've set up your build environment correctly, complaining at Intel (again) :-) Mark On Sun, Aug 25, 2013 at 7:18 AM, Nimmy McNimmerson wrote: > Hi, > > Apparently this is an issue with my intel compiler; the dyna

Re: [gmx-users] 'Command not found' after installation

;Trace/BPT trap: 5 > >If I try 'pdb2gmx', it says: > >dyld: Library not loaded: libiomp5.dylib >  Referenced from: /usr/local/gromacs/bin/pdb2gmx >  Reason: image not found >Trace/BPT trap: 5 > >Did the installation not work properly? > > >

[gmx-users] 'Command not found' after installation

Hello all, I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I downloaded the latest Intel C++ compilers and built Gromacs successfully (at least it appeared to be successful since I saw no error messages). I appended this line to my ~/.profile file: source /usr/local/gromacs