Re: [gmx-users] Gromacs on Stampede

2013-10-12 Thread Arun Sharma
greatly appreciated.  Thanks, On Friday, October 11, 2013 5:31 AM, Arun Sharma wrote: Dear Chris, Thank you so much for providing the scripts and such detailed instructions. I was trying to load the gromacs module that is already available and was unable to get it to run.  Thanks to you, I

Re: [gmx-users] Gromacs on Stampede

2013-10-11 Thread Arun Sharma
Dear Chris, Thank you so much for providing the scripts and such detailed instructions. I was trying to load the gromacs module that is already available and was unable to get it to run.  Thanks to you, I now have a working gromacs installation. On Thursday, October 10, 2013 2:59 PM, Christ

[gmx-users] Gromacs on Stampede

2013-10-10 Thread Arun Sharma
Hello, Does anyone have experience running gromacs and data analysis tools on Stampede or similar supercomputer. Do we have a set of best practices or approaches for this situation. Any input is highly appreciated. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

[gmx-users] Minimum distance periodic images, protein simulation

2013-09-20 Thread Arun Sharma
Hello, I ran a 100-ns long simulation of a small protein (trp-cage) at an elevated temperature. I analysed the distance between periodic images using g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi The output shows that there are situations when the closest dis