Re: [gmx-users] doubt in remd

2013-04-09 Thread Mark Abraham
On Tue, Apr 9, 2013 at 8:29 AM, Shine A wrote: > Respected sir, > > I successfully completed REMD simulation. Now I am > struggling with analysis part. Here how I select the global minimum from > replica? Can you give some suggestions about the analysis part? Doing a simulat

Re: [gmx-users] doubt in remd

2013-04-09 Thread Simone Conti
Hi! I'm also working on REMD in these days. For temperature spacing you can use this web site: http://folding.bmc.uu.se/remd/ In order to find the most probable structure, which should be the global minimum, I think you can work with cluster analysis based on rmsd. Or it can be also useful a second

Re: [gmx-users] doubt in remd

2013-04-09 Thread Erik Marklund
The gromacs web page links to this server for REMD temperature generation: http://folding.bmc.uu.se/remd/ On 9 Apr 2013, at 08:34, Nikunj Maheshwari wrote: > Hi. Glad to know that your REMD was successful. We are trying to do the > same, but are stuck in between. > Can you tell us, how did you

Re: [gmx-users] doubt in remd

2013-04-08 Thread Nikunj Maheshwari
Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A wrote: > Respected sir, > > I successfully completed REMD sim

[gmx-users] doubt in remd

2013-04-08 Thread Shine A
Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.