AW: Tutorial example of replica exchange

From: Norman Geist (
Date: Thu Mar 10 2016 - 02:03:38 CST



1) The jobX.conf will just put together the *_base.namd the *_remd.namd and and will source the replica.namd script which actually does the REMD. Also it is used to source additional restart.files from job1 and higher. You will get output files named like the job. So it’s just some kind of output separation if you want to restart the simulation multiple times.

2) Shouldn’t you specify how many processes to launch or threads to use? Otherwise try to use a non GPU version an see if it helps. There’s seems to be a problem with CUDA REMD, especially when using GBIS.


Let us know


Norman Geist


Von: [] Im Auftrag von Dr. Eddie
Gesendet: Dienstag, 8. März 2016 23:56
Betreff: namd-l: Tutorial example of replica exchange


Hi all,

I am trying to learn how to REMD with namd 2.11 by following the (spartan) tutorial <> . I have two problems:

1) I don't understand what jobX.conf are doing exactly and why two are commands are needed (first job0.conf then job1.conf)

2) I can't get it to run:

~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ mpirun ./../../namd2 +idlepoll +replicas 8 job0.conf +stdout output/%d/job0.%d.log

Charm++: standalone mode (not using charmrun)

Charm++> Running in Multicore mode: 1 threads


mpirun noticed that process rank 0 with PID 23811 on node heartofgold exited on signal 11 (Segmentation fault).



Nothing comes out so I can't see any errors:


~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ ls output/*


total 0



total 0



total 0



total 0



total 0



total 0



total 0



total 0



I've tried using +idlepoll since this is a gpu build, but this changed nothing. Any help or idea would be most welcome!



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