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[ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding
From: |
Arash Azari |
Subject: |
[ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding |
Date: |
Mon, 1 Apr 2013 08:26:19 -0700 (PDT) |
Hello everyone,
I am using the nightly build of
ESPResSo (3.2 , 8 of March as I remember). I have a couple of
questions and appreciate any recommendation (I have checked the
mailing list archive with a combinations of keywords, but could not
find my answers; sorry if the answers are already there).
- I compiled it with the BOND_ANGLE
option, but inter command output recognizes all the bond angle
potentials as an “unknown”. I thought it is not very important
because simulation looks fine in terms of the bond angle potential
behaviour. The problem is that when I am using the blockfile to
create an output file, ESPResSo cannot recognize the interaction
type (defined as an unknown in output file). Is it a bug?
- I could not find proper
documentation on the restarting the simulation. When I am using the
blockfile as an input, what quantities or parameters should be
rewritten in the configuration file (Tcl)? Should I keep most of the
parts (box size, time-steps, interactions ...) except the “part”
or “polymer” commands? What about changing the simulation
parameters in new run? For example using different ensemble
NVT-->NPT, time-steps, changing the interactions (deleting or
adding), changing the box size and so on.
- During the warm-up, does the
thermostat (e.g. Langevin) works or it is just the energy
minimization at fixed temperature? I mean can I de/increase the
temperature during the warm-up gradually?
-I compiled the ESPResSo with the
required features (COLLISION_DETECTION and VIRTUAL_SITES_RELATIVE)
to use the dynamic bonding, but I receive the “invalid command
name "collision_detection" “ error message? I used
single CPU to run this dynamic bonding simulation. Could you please
point out my mistake?
- Is it possible to manually delete
all or some of the the bonds which are created during the dynamic
bonding simulation? I mean when we restart the simulation not during
the same simulation.
I highly appreciate any recommendation
and help.
Thank you,
Cheers,
Arash
Arash Azari
- [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding,
Arash Azari <=
- Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding, Rudolf Weeber, 2013/04/01
- Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding, Arash Azari, 2013/04/03
- Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding, Axel Arnold, 2013/04/03
- Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding, Arash Azari, 2013/04/03
- Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding, Axel Arnold, 2013/04/04