Hello again,
I am wondering if anyone has encountered this before. Basically what I am
trying to do is this :
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
to calculate binding energy of a ligand to protein. I have done almost all
the steps, however, i would like also to do long range dispersion
correction. In order to do this, you have to rerun your simulation at
lambda = 1 and lambda = 0 with different cut-offs (eg. 9A and 30A). In
other words, I want to calculate energy of a system at each step within
certain trajectory using cutoff1 = 9A and cutoff2 = 10A and compare the
results. However, I have not found any way to do this. I assume to somehow
utilize imin=5 with thermodynamic integration (I have done calculations
using pmemd, but pmemd does no support imin=5), and sander.
Thank you very much for any advice,
Vlada
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Received on Thu Apr 02 2015 - 04:00:09 PDT
