[gmx-developers] A minor bug in demux.pl
Piggot T.
T.Piggot at soton.ac.uk
Sun Jul 7 10:35:26 CEST 2019
Hi,
This is a known problem, see:
https://groups.google.com/forum/m/#!topic/plumed-users/XhB34MmSpjM
There’s also a modified script provided there too that I’ve used without problem for long trajectories.
I guess the script provided by GROMACS should be updated. It is probably worth reporting it on redmine.
Cheers
Tom
On 7 Jul 2019, at 07:05, Yong Wang <wyongciac at gmail.com<mailto:wyongciac at gmail.com>> wrote:
Hi,
We are running a normal REMD with 10 replicas and an exchange frequency of 0.2ps, and tried to use demux.pl<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C525a9452f6c6459d41ab08d702a113ed%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=1Ul2988Phdxj8SNDMS0MxfKrp00b7oE8r069UaN1dFI%3D&reserved=0> to get continuous trajectories. But we found the demuxed trajectories always become discontinuous after 100ns. After some frustrating debugging, we found the replica index file (replica_index.xvg) was not corrected generated by demux.pl<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C525a9452f6c6459d41ab08d702a113ed%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=1Ul2988Phdxj8SNDMS0MxfKrp00b7oE8r069UaN1dFI%3D&reserved=0>. For example, the output looks like this:
99998.8 9 2 4 0 5 8 3 7 6 1
99999 9 2 4 0 8 5 7 3 6 1
99999.2 9 2 4 8 0 5 7 3 6 1
99999.4 9 2 8 4 5 0 7 3 1 6
99999.6 9 2 8 5 4 0 7 3 1 6
99999.8 9 2 8 5 4 0 7 3 6 1
100000 9 2 8 4 5 0 7 3 6 1
100000 2 9 8 4 0 5 7 3 6 1
100000 2 9 8 0 4 5 7 6 3 1
100001 9 2 0 8 5 4 7 6 3 1
100001 9 2 0 8 5 4 7 3 6 1
100001 2 9 8 0 4 5 3 7 1 6
100001 2 9 8 4 0 5 3 7 1 6
100001 2 9 4 8 0 5 7 3 1 6
100002 2 9 4 0 8 5 7 3 1 6
100002 2 9 0 4 8 5 3 7 6 1
100002 2 9 0 8 4 5 3 7 6 1
100002 2 9 8 0 4 5 3 7 6 1
100002 2 8 9 4 0 5 3 7 6 1
As you can see, the time information in the first column was confused after 100000 (corresponding to 100ns). So we tried to correct the time information, and the problem seems solved. In our case, we made minor modifications on the demux.pl<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdemux.pl&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C525a9452f6c6459d41ab08d702a113ed%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=1Ul2988Phdxj8SNDMS0MxfKrp00b7oE8r069UaN1dFI%3D&reserved=0> script by simplify replacing "%-20g" by "%-20.1f". And it works for us!
I don't know if this is the best solution but I am reporting this and hope it is helpful to others. And the issue can only occur when we use an exchange frequency smaller than 1ps and run the simulation longer than 100ns. Could you identify if this is a minor bug or just limited to our case? Thanks a lot!
Regards,
Yong
--
==========================
Yong Wang
Postdoc in Lindorff-Larsen Lab
Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science
Department of Biology, University of Copenhagen
Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
https://scholar.google.com/citations?hl=en&user=LblGaZMAAAAJ&view_op=list_works&sortby=pubdate<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailtrack.io%2Ftrace%2Flink%2F01603ac90f476741fe794a895a94d4ee843620d6%3Furl%3Dhttps%253A%252F%252Fscholar.google.com%252Fcitations%253Fhl%253Den%2526user%253DLblGaZMAAAAJ%2526view_op%253Dlist_works%2526sortby%253Dpubdate%26userId%3D2367320%26signature%3D0578092a37df8130&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C525a9452f6c6459d41ab08d702a113ed%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=ARI9X4fG31JzV%2BXe58F1FA3jOdjCE4K%2FIJ%2BZjJl92kE%3D&reserved=0>
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