Hello,
I’m modeling a carboxylic acid (palmitoleic and linoleic acids) and having
issues with my MD simulations. I used the RESP methodology along with
antechamber to get the necessary .prep and .frcmod files. I was able to
successfully create a box (~25,000 atoms) for each carboxylic acid using
packmol and tleap. I was also able successfully minimize the structure
prior to starting my NPT simulations. The simulations seem to start out
fine but they crash with the energy, temperature and the VDW contributions
to the energy increasing. I also noticed that when “wrapping first mol”
appears for the first time in the md.out file, then my mdcrd and rst-crd
file turn to ‘****’. I have tried turning iwrap off and the problem still
occurs. Also I’m unable to use VMD to see what is happening since the mdcrd
file is filled with ‘******’. I have attached my input and output files.
I’m using Amber 12 with all of the bug fixes.
Thanks,
Ben
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Received on Wed Jun 12 2013 - 14:30:03 PDT
