Hello all
I am doing MMPBSA analysis for protein-DNA complex. I have 4 trajectory of 5ns
each and I have catenate them to 20ns trajectory.
I have done hydrogen bond analysis of complete 20ns trajectory but binding free
energy calculation of only 10ns.
Will it affect my result if I compare my 20ns hydrgen bond analysis with 10ns
calculated bindg free enrgy?
Or should I use complete 20ns trajectory for binding free energy calculation.
One more thing I have used nminterval=100, is it too lagre?
since nmode calculation is time taking so I have used this large value of
nminterval.
With regards
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Oct 04 2011 - 10:30:05 PDT
