On Thu, Sep 15, 2016, Batuhan Kav wrote:
>
> I’m recently working on some simulations where I altered LJ interactions
> between specific atom types. For that, I used changeLJPair in
> parmed. When I run my simulations with pmemd.MPI or pmemd.cuda (Amber
> 14), out file contains an info line saying
>
> INFO: Off Diagonal (NBFIX) LJ terms found in prmtop file.
> | The prmtop file has been modified to support atom
> | type based pairwise Lennard-Jones terms.
>
> and the simulation proceeds without any errors/crashes. However, this
> info message confused me a bit. Does this message say my changes have
> been modified by pmemd to original values, or is it just a warning for
> existence off-diagonal terms?
The latter: just notifying you that off-diagonal terms are present.
>
> Lastly, through mail list, I found an old thread
> (http://archive.ambermd.org/201311/0135.html
> <http://archive.ambermd.org/201311/0135.html>) informing that in Amber
> 12 it is not possible to use changeLJPairs with pmemd.cuda. Just to be
> sure, did this change in Amber 14?
If you are getting the INFO message listed above, that means the program knows
what to do with off-diagonal terms.
....dac
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Received on Fri Sep 16 2016 - 02:30:04 PDT
