From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Oct 26 2015 - 03:21:01 CDT
Replica.namd will do everything basically.
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). All replicas will use the jobscribt from 1. And source replica.namd which sources the remd.conf. Each replica has an identifier replica-id and will be assigned a starting temperature from the given range.
5. Now each replica will have the following loop:
a. Run stepsperrun
b. Communicate potential energy via replicasend/replicarecv to even/uneven replica neighbor
c. Decide exchange based on metropolis cretarion
d. Do exchange temperature/or not
e. Incr i_run
f. Goto a: until i_run == num_runs
You may not confuse the “new” replica exchange implementation based on replicasend/resv commands with the old tcl server implementation which started new namd simulations and exchanged restart files.
Von: Jessen Lucas [mailto:jessenlucas0_at_gmail.com]
Gesendet: Montag, 26. Oktober 2015 08:26
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: namd-l: replica exchange module
Thanks Norman, Is there any explanation for that, I feel confusion about it, I saw source $namd_config_file in replica.namd, if it not work at each timestep, how does it run MD in each replica?
2015-10-26 15:11 GMT+08:00 Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >:
No. Please check the example simulation that comes with the namd source.
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Jessen Lucas
Gesendet: Montag, 26. Oktober 2015 07:30
An: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: replica exchange module
Dear NAMD users,
I want to use replica exchange module, I read codes in replica.namd and swarm.namd from tutorial files.
I was confused about how to set up and run each replica configuration. my diea is
temperature 300 + $replica_id
So will source $namd_config_file every MD timestep? I do not what the workflow is in here.
Is it right? I am new to NAMD, please give me some suggestion of replica exchange module.
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