Project

General

Profile

Feature #1486

Request for more precision in the replica exchange timestep output

Added by Chris Neale about 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
mdrun
Target version:
-
Difficulty:
uncategorized
Close

Description

In the log file, the timestep is output in a way that can be lossy. Here is an example of some output that I got after running for > 1 us / replica and attempting exchanges every 1 ps:

Replica exchange at step 484096500 time 968193
Replica exchange at step 484097000 time 968194
Replica exchange at step 484097500 time 968195
...
Replica exchange at step 538320500 time 1.07664e+06
Replica exchange at step 538321000 time 1.07664e+06
Replica exchange at step 538321500 time 1.07664e+06

Then, demux.pl can not process the trajectories.

User aperez has provided a solution by modifying demux.pl :
http://gromacs.5086.x6.nabble.com/REMD-demux-after-100-ns-per-replica-tp5015885.html

but ideally the log file would have a unique time if it is going to print one.

One solution is to modify src/kernel/repl_ex.c .

In version 4.6.1, line 907 uses %g for output, when %.15e would ensure that even if a user attempted exchanges every 0.5 fs, then the information would be lossless up to 0.5 seconds of simulation (provided that the value that is being printed even has this much precision).

Chris.

Associated revisions

Revision 02d4d55d (diff)
Added by Rossen Apostolov almost 3 years ago

Print in higher precision repl_ex timestep.

Fixes #1486.

Change-Id: Ibe5bcee18f761bea96e1b4a432774a4472a40f47

Revision 3b90030c (diff)
Added by Berk Hess almost 3 years ago

Made repl_ex time step more readable

A recent change made the repl_ex time print %e, now it's %.5f,
as in the log file.

Refs #1486.

Change-Id: I2e669d91a61e6a696ce6d123c701fa8b773a3c2f

History

#1 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1486.
Uploader: Rossen Apostolov ()
Change-Id: Ibe5bcee18f761bea96e1b4a432774a4472a40f47
Gerrit URL: https://gerrit.gromacs.org/3566

#2 Updated by Rossen Apostolov almost 3 years ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 100

#3 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1486.
Uploader: Berk Hess ()
Change-Id: I2e669d91a61e6a696ce6d123c701fa8b773a3c2f
Gerrit URL: https://gerrit.gromacs.org/3568

#4 Updated by Rossen Apostolov almost 3 years ago

  • Assignee deleted (Berk Hess)

#5 Updated by Rossen Apostolov almost 3 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF