Re: [AMBER] Simulations Without Network

From: Garcia, Mauro <>
Date: Fri, 27 Mar 2020 22:31:29 +0000


After assessing where the problems were occurring in the script, the error displayed once it got to the MMPBSA calculations, in which I use Thank you Gustaf and Dave, for the information and guidance on this error message. I have successfully connected the computer to a network and it seems to be working now for my simulations and binding free energy calculations!

Best regards,

On 3/27/20, 3:22 PM, "Gustaf Olsson" <> wrote:

    Hello Mauro
    As Dave pointed out, ignoring the capability of installing updates and potentially some particular programs you do not need network access to set-up, run and evaluate simulations using antechamber, parmchk2, leap, cpptraj and sp forth. Assuming everything is already compiled and all dependencies needed already installed.
    However, I have on several occasion noticed that trying to run MPI tests on my mac produced a cascade of firewall notifications. Same thing running in WSL where Windows firewall had a complete meltdown together with real time monitoring and totally halted the tests.
    If you are trying to execute sander.MPI or pmemd.MPI and have problems with it, try just running the regular sander or pmemd. If this then runs, my guess is that you have a firewall/antivirus instance blocking what I think is internal TCP traffic, which seems to be utilized by the MPI programs.
    Best regards
    // Gustaf
    Från: David Cerutti <>
    Skickat: den 27 mars 2020 17:56:55
    Till: AMBER Mailing List
    Ämne: Re: [AMBER] Simulations Without Network
    If Amber is installed on your machine, barring the need to install updates,
    it should work to run pmemd, sander, and other major programs without
    network access. The major engines do not need to reach out and get force
    fields from an encrypted server like Maestro, but I can't speak for every
    program in the package.
    On Fri, Mar 27, 2020 at 12:35 PM Garcia, Mauro <> wrote:
> Dear All,
> My research lab has relocated our computers that have the AMBER software
> on them. I tried running a simulation, as I normally do (this time
> off-campus) and I get the error message, “No network interfaces were found
> for out-of-band communications. We require at least one available network
> for out-of-band messaging.” However, after speaking to one of our
> collaborators, they were still able to run simulations while not being
> connected to a network, so I do not suspect it is a networking issue
> because most software works without internet once it is installed. Any
> ideas of how I may troubleshoot and correct this error message?
> We have tried to connect our system via ethernet at my apartment but
> cannot connect here. The question is, is it necessary to connect to a
> network to run simulations and energy calculations on AMBER18?
> Best regards,
> Mauro A. Garcia
> Master of Science in Chemistry, TAMUCC ‘21
> Computational Chemistry Graduate Research Student, Billiot Lab
> Graduate Teaching Assistant, Department of PENS
> _______________________________________________
> AMBER mailing list
    AMBER mailing list
    AMBER mailing list

AMBER mailing list
Received on Fri Mar 27 2020 - 16:00:02 PDT
Custom Search