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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 The docs are outdated to this point.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 outdated because there is no other reference to Espresso_bin in the user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 Košovan
> 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.
> >