Hello,
I am interested in scaling all vdW interactions and am looking for the most appropriate method to accomplish my task. My preference would be to scale using epsilon, however, my attempts at doing this from within python has failed, here is some sample code:
Import parmed as pmd
prmtop=pmd.load_file('prmtop')
for a in prmtop.atoms:
a.epsilon=1.1*a.epsilon
prmtop.save('newprmtop')
I have also attempted a few things within parmed but this option only seems to allow editing one by one and modifying 20k+ atoms seems tedious. Lastly, I am currently editing the LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF by hand scaling all values by 1.1, but, again this seems to me not the standard method of accomplishing this. In my past I have used Desmond and gromacs and there it is simple to scale epsilon and I am hoping there is something similar in amber that is not well documented. Any help would be greatly appreciated since the post calculations I need to perform are written for use with amber prmtop and trajectory files.
Thank you in advance!
With best,
Korey
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Received on Tue Jul 03 2018 - 11:30:02 PDT
