From: Jessen Lucas (jessenlucas0_at_gmail.com)
Date: Tue Oct 27 2015 - 03:42:23 CDT
Thank you, I will try it.
2015-10-27 16:08 GMT+08:00 Norman Geist <norman.geist_at_uni-greifswald.de>:
> Basically by modifying replica.namd, you can treat each replica
> individually, as it can be identified by replica_id. You just need to
> understand that replica.namd plays in jobscript context, whereas tclforces
> plays in tclforces context. It's not the same TCL context. But you could
> give each replica a different tclforces configuration, which I hope can be
> changed between "run" commands.
> Norman Geist
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Jessen Lucas
> Gesendet: Dienstag, 27. Oktober 2015 04:49
> An: Norman Geist <norman.geist_at_uni-greifswald.de>
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: replica exchange module
> Hello, Dear Norman,
> I am sorry to disturb you again, if I want to add different force to
> different replicas, then should I do like the following,
> add the following codes (tclforces on, tclforcescript tclforce.tcl) in
> step 5 you mentioned above. how about colvar bias scriptfunction in each
> replica if the scriptfunction in replica 1 is different from replica 2?
> actually, what I want to do is to write code in each replica, so all this
> could be done in step 5?
> Thanks a lot.
> J. Lucas
> 2015-10-26 16:21 GMT+08:00 Norman Geist <norman.geist_at_uni-greifswald.de>:
> > Replica.namd will do everything basically.
> > Workflow:
> > 1. Use make_output_dirs to create the replicas individual output
> > folders
> > 2. Create a general jobscript without some like run/numsteps or
> > temperature that are set by replica.namd later when sourced.
> > 3. Replica.namd itself needs some options to be set like
> > stepsperrun, runsperframe etc.. Therefore you create a remd.conf which
> > replica.namf will source
> > 4. You start namd with +replicas option which which will run that
> > number of individual namd simulations (number of nodes/cores/gpus should
> > devisible by number of replicas, you need at least two cores per
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