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

2013-10-22 Thread Nimmy McNimmerson
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

2013-08-25 Thread Nimmy McNimmerson
and iomp5 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 nimzs...@yahoo.com wrote: Hi, Apparently this is an issue with my intel compiler

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

2013-08-25 Thread Nimmy McNimmerson
That worked! Thanks a ton! From: Justin Lemkul jalem...@vt.edu To: Nimmy McNimmerson nimzs...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, August 25, 2013 2:54 PM Subject: Re: [gmx-users] 'Command not found' after

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

2013-08-24 Thread Nimmy McNimmerson
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

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

2013-08-24 Thread Nimmy McNimmerson
McNimmerson nimzs...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, August 24, 2013 10:42 AM Subject: Re: [gmx-users] 'Command not found' after installation Try g_luck. That's what has worked for me. On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote: Hello all