Optimizing force-field with AmberTools for small organic molecules in water
dr.bra... at gmail.com
dr.bra... at gmail.com
Fri Dec 22 00:36:16 UTC 2017
Dear ALL,
I have problems with preparing system for ab initio molecular dynamic
simulation of phenyletilamine (PEA). I need to do something similar to
this: https://www.cp2k.org/exercises:2015_cecam_tutorial:urea but with PEA
and pure AIMD, not QM/MM. I have issues with first part, to be more
accurate I'm failing to reach the point where I can use files
Files/mol_solv.crd
<http://cp2k.org/static/exercises/2015_cecam_tutorial/UREA/Files/mol_solv.crd>
and Files/mol_solv.top
<http://cp2k.org/static/exercises/2015_cecam_tutorial/UREA/Files/mol_solv.top> which
are obtained with leap. I've tried to follow all kind of tutorial on the
web, but they are all connected to larger systems, such as protein ones.
None of them is dealing with these small organic molecules such PEA.
I'd really appreciate if somebody could point me directions how to reach my
goal since I',m beginner with these things. It does not have to be
AmberTools software package to reach my goal to be clear.
Thanks in advance!!
Bests,
Bane
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