Re: [gmx-users] Questions regarding REMD simulation

2011-09-18 Thread Mark Abraham
On 18/09/2011 9:35 PM, michael zhenin wrote: Hi All, I have few questions regarding REMD simulation. I assume REMD works in the following way: Each replica starts with a given temperature and the temperature of each replica changes along the simulation (as described in Sugita and Okamoto pub

Re: [gmx-users] Questions regarding REMD simulation

2011-09-18 Thread SebastianWaltz
Hi, in the GROMACS implementation of REM the trajectories are exchanged not the temperatures. The temperatures are kept constant. As well as the description of the Okamoto paper cited by GROMACS Basti On 09/18/2011 01:35 PM, michael zhenin wrote: > Hi All, > > I have few questions regarding REM

RE: [gmx-users] Questions regarding REMD simulation

2011-09-18 Thread gal.fradin
users@gromacs.org Subject: [gmx-users] Questions regarding REMD simulation Hi All, I have few questions regarding REMD simulation. I assume REMD works in the following way: Each replica starts with a given temperature and the temperature of each replica changes along the simulation (as desc

[gmx-users] Questions regarding REMD simulation

2011-09-18 Thread michael zhenin
Hi All, I have few questions regarding REMD simulation. I assume REMD works in the following way: Each replica starts with a given temperature and the temperature of each replica changes along the simulation (as described in Sugita and Okamoto publication, 1999). Then demux.pl and trjcat collect