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Re: [ESPResSo-users] Espresso_bin and mpirun


From: Olujide Olubiyi
Subject: Re: [ESPResSo-users] Espresso_bin and mpirun
Date: Wed, 24 Aug 2011 18:47:27 +0200

Thanks everyone. 

I have been able to submit the job although it is finding it difficult to link 
up to the cores:

 "waiting for 15 more clients"

I am not yes certain if this has anything to do with espresso or with the 
cluster I am working on.

I am running espresso with peptideB, and this is the command I used:

$PATH-to/mpiexec -n 1 $PATH-to/Espresso $PATH-to/peptidebuilder.tcl 
myconfig.tcl -espresso -replica

I have 16 cores on the computer node (already defined in an mpd.hosts file) I 
am attempting to use 
for the simulation. Here is the content of my myconfig.tcl file:

set amino_acids {
    {LYS LEU VAL PHE PHE ALA}
    {LYS LEU VAL PHE PHE ALA}
    {LYS LEU VAL PHE PHE ALA}
    {LYS LEU VAL PHE PHE ALA}
}

# Model oxygens and N-hydrogens - "on" or "off"
set display_O_H "on"


# Directory and filenames for output
set directory "REPX"
set PDB_file "$directory"
set filenumber 0



set espresso_switch "on"
set setbox_l {43.24 43.24 43.24}
set warm_time_step 0.01
set main_time_step 0.01
set verlet_skin 0.4
set langevin_gamma 1.0
set systemtemp [expr 1.0*$eps]

# electrostatics
set charges "off"

# The number of steps to integrate with capped forces
set warm_steps 500
# The number of times to call warmup    #total equilibration of 1ns
set warm_n_times 200


# OPTION #2: If replica flag is set
# Set the replica exchange temperatures

#300 K = 1.00
set replica_temps { 0.67 0.71 0.75 0.79 0.84 0.89 0.94 0.99 1.05 1.11 1.17 1.24 
1.31 1.39 1.47 1.55 }

# number of times to integrate between each replica MC step
set replica_timestep 1000
# number of replica exchange rounds
set replica_rounds 500000
# frequency at which replica pdb files are written
set replica_pdb_freq 10


I will appreciate your advice.

Best regards,

Olujide Olubiyi

German Research School for Simulation Sciences,
Germany.


On 08/24/11, Peter Kosovan  <address@hidden> wrote:

> Hi Olujide
> 
> The docs are outdated to this point. More precisely, the docs for mbtools are 
> outdated because there is no other reference to Espresso_bin in the user 
> guide. In earlier versions "Espresso" used to be a wrapper script which tried 
> to figure out some of your settings and then launched the actual binary 
> executable called "Espresso_bin". Now the wrapper script has been removed and 
> "Espresso" is the actual binary executable. If you cannot launch it, your 
> problem lies somewhere else.
> 
> To understand your problem, it would be desirable that you send the command 
> which you use to launch Espresso and the error message you get.
> 
> peter
> 
> --
> Peter KoŇ°ovan
> Institute of Computational Physics
> University of Stuttgart
> Pfaffenwaldring 27
> 70569 Stuttgart
> Germany
> 
> On Wed, 24 Aug 2011, Olujide Olubiyi wrote:
> 
> >Hello everyone,
> >
> >I attempted to perform an REMD simulation but could not using the Espresso 
> >executable. I
> >read that this might be remedied using Espresso_bin instead. But I could not 
> >find Espresso_bin
> >in my espresso-3.0.0 distribution. Could someone please provide me 
> >information on how to get
> >Espresso_bin. I couldn't find any such direction in the users' guide.
> >
> >
> >Thanks
> >Olujide Olubiyi
> >German Research School for Simulation Sciences
> >Germany.
> >



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