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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
        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,


Arash Azari 

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