Re: [gmx-users] issue in replica exchange

2013-05-02 Thread Simone Conti
I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add

Re: [gmx-users] issue in replica exchange

2013-05-02 Thread Simone Conti
you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote: I'm running remd in NPT ensemble for a small peptide and all is ok

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