[gmx-users] REMD temperature trajectory

[Nawel Mele]

Dear Gromacs user,

I performed a REMD simulation and I want to analyse my result per temperature.
I am interested at looking the trajectory for the lowest and the
highest temperature.
I am used to perform REMD with Amber and I realised that Amber
exchanges temperature during the simulation,compare to Gromacs which
returns a discontinuous trajectories
for each temperatures.
So my question is , do I need to use the demux.pl script to get a
"temperature trajectory" or can I, from the log output file, just
create a trajectory
at the temperature of interest?
For example if I am interested on the lowest temperature, should I
just need to analyse the prod0.log file??

Another question, the output replica_temp.xvg from the demux.pl looks
like this :

0                       0    1    2    3    4    5    6    7    8    9
  10   11   12   13   14   15   16   17   18   19   20   21   22   23
 24   25   26   27   28   29   30   31   32   33   34   35   36   37
38   39   40   41   42   43   44   45   46   47
2                       1    0    2    3    5    4    6    7    8    9
  10   11   13   12   14   15   16   17   18   19   21   20   23   22
 24   25   27   26   28   29   31   30   33   32   34   35   37   36
39   38   41   40   43   42   44   45   46   47
4                       2    0    1    3    6    4    5    8    7   10
   9   11   13   12   14   15   16   17   18   20   22   19   24   21
 23   26   28   25   27   30   32   29   33   31   34   35   37   36
40   38   41   39   44   42   43   46   45   47
6                       3    1    0    2    6    4    5    9    7   11
   8   10   12   13   15   14   16   17   19   20   22   18   24   21
 23   27   29   25   26   30   32   28   33   31   34   35   37   36
41   39   40   38   45   43   42   47   44   46


Does that mean that, except for the first column, each column
corresponds to each temperature? An so from that we can follow the
trajectory of the replicas for a temperature of interest?

Many thanks in advance

Nawel


-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ