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

[Mark Abraham]

On Tue, Apr 14, 2015 at 2:50 AM, 14110220035 at fudan.edu.cn <
14110220035 at fudan.edu.cn> wrote:

> 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
> )?
>

Yes. In REMD trajectories, you must choose whether you want a continuous
trajectory or a continuous ensemble. mdrun writes the latter.

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 .


When? And when did it exchange back? And how do those compare to the time
stamps in the left-hand column? There's nothing to demux if there had been
no net exchange on replica 0 by the time output was written.

Mark


> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.