[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