[gmx-users] Post-Processing on the REMD trj

[14110220035 at fudan.edu.cn]

Dear users,
  
                Rescently, I used  REMD to do some simulation by Gromacs , I konw GROMACS exchanges coordinates. So does this means every trajectory was written at a temperture ?AND if i want to analyse the lowest temperature,  can I  just analyse md0.xtc as  'trajectory no longer be continuous'(http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations:_Mark_Abraham,_Session_1B)? 

secondly， the Perl script demux.pl can  analyse a single REMD .log file and writes two special .xvg files .But  i got some problem ,as we can see blow ,
0                       0    1    2    3    4    5    6    7    8    
4                       0    1    2    3    4    5    6    7    8   
8                       0    1    2    3    4    5    6    8    7   
12                      0    1    2    4    3    5    6    8    7    
16                      0    1    2    4    3    5    6    8    7   
20                      0    1    2    4    3    6    5    8    7   
24                      0    2    1    4    3    5    6    7    8   
28                      0    2    1    4    3    5    6    7    8   
32                      0    2    1    4    3    5    6    7    8   
36                      0    2    1    4    3    5    6    7    8   
40                      0    2    1    4    3    5    6    7    8   
44                      0    2    1    3    4    5    6    7    8    
48                      0    2    1    3    4    5    6    7    8   
52                      0    1    2    4    3    5    6    7    8   
56                      0    1    2    4    3    5    6    7    8   
60                      0    2    1    3    4    5    6    7    8    
64                      0    1    2    3    4    5    6    8    7    
68                      0    1    2    3    4    5    6    8    7    
72                      0    1    2    3    4    5    6    8    7    
76                      0    1    2    3    4    5    6    8    7    

the 0 didn't exchange ,however the log describes the 0 did exchange . i think my log produced by gromacs4.6.5 doesn't match the  Perl script demux.pl. Can someone tell me how to modify the  Perl script demux.pl.?


thank you 

Dongdong Wang


--
Dongdong Wang
Chemistry Department
Fudan University
200433, Shanghai
P.R. China
Tel:+86 15121115863
Email: 14110220035 at fudan.edu.cn