[gmx-users] g_rdf

2013-03-30 Thread mohammad agha
Dear Gromacs Specialists, I want to find information about RDF of some components in my system but when I do the g_rdf command, I find true answers about RDF diagrams but my system type below note in several times: There were 2 inconsistent shifts. Check your topology May I know that this

[gmx-users] About the configuration of Gromacs on multiple nodes with GPU

2013-03-30 Thread 崔学文
I'm running Gromacs 4.6.1 on 2 nodes with 3 GPUs(2 on host1,1 on host2, all nvidia K20c), and I'm using openMPI 1.6.4 to let Gromacs run parallel on 2 nodes. However, I found that Gromacs can only find the GPUs on the local node which it's launched, it can't automatically use the GPUs on the

Re: [gmx-users] About the configuration of Gromacs on multiple nodes with GPU

2013-03-30 Thread Szilárd Páll
Hi, You can certainly use your hardware setup. I assume you've been looking at the log/console output based on which it might seem that mdrun is only using the GPUs in the first (=master) node. However, that is not the case, it's just that the current hardware and launch configuration reporting

[gmx-users] how to install the gromacs 4.6.1 using the intel icc and ifor

2013-03-30 Thread aixintiankong
Dear, I have install intel icc and ifor on my system centos, and i want to install gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use to indicate the icc and ifor when i install the gromacs. thank you very much! At 2013-02-21 13:00:55,aixintiankong

Re: [gmx-users] how to install the gromacs 4.6.1 using the intel icc and ifor

2013-03-30 Thread Justin Lemkul
On 3/30/13 10:21 AM, aixintiankong wrote: Dear, I have install intel icc and ifor on my system centos, and i want to install gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use to indicate the icc and ifor when i install the gromacs. -DCMAKE_C_COMPILER=icc

[gmx-users] semi isotropic settings

2013-03-30 Thread Elisabeth
Hi all, I wanted to use Pcoupltype = semiisotropicbut I am not clear about the compressibility settings if I want to keep Z directions fixed in my system and letting X and Y change. Which case 1 or 2 is correct for semi isotropic option? 1) compressibility = 3.5e-5 3.5e-5 0 2

Re: [gmx-users] semi isotropic settings

2013-03-30 Thread Justin Lemkul
On 3/30/13 11:39 AM, Elisabeth wrote: Hi all, I wanted to use Pcoupltype = semiisotropicbut I am not clear about the compressibility settings if I want to keep Z directions fixed in my system and letting X and Y change. Which case 1 or 2 is correct for semi isotropic option? 1)

Re: [gmx-users] semi isotropic settings

2013-03-30 Thread Elisabeth
Hi Justin, The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two. If thats nto the case I guess compressibility = 3.5e-5 0 is the correct value. What do you think? On 30 March 2013 11:41, Justin Lemkul jalem...@vt.edu wrote: On 3/30/13 11:39 AM, Elisabeth wrote: Hi

Re: [gmx-users] semi isotropic settings

2013-03-30 Thread Justin Lemkul
On 3/30/13 11:47 AM, Elisabeth wrote: Hi Justin, The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two. No, it is not a ratio. The use of x/y simply means both x and y. If thats nto the case I guess compressibility = 3.5e-5 0 is the correct value. What do you

[gmx-users] Free energy landscape by g_sham

2013-03-30 Thread Kavyashree M
Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- gmx-users mailing listgmx-users@gromacs.org