Dear All,
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?
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?
Best,
Batuhan
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Received on Thu Sep 15 2016 - 14:00:02 PDT
