Re: replica exchange module

From: Jessen Lucas (jessenlucas0_at_gmail.com)
Date: Tue Oct 27 2015 - 03:42:23 CDT

Thank you, I will try it.

Best regards,
J. Lucas

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
>
> -----Urspr√ľngliche 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
> be
> > devisible by number of replicas, you need at least two cores per
> replica)=
>
>

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