Hi all,
I have a basic question regarding calculation of entropy and MMPBSA calculation. I did 10ns MD on two complexes and now want to calculate free binding energy.
So I want to calculate MMPBSA from 10000 frame with an interval of 10 (i.e total 1000 frame) and entropy of 20 frame..(Is it okay to estimate entropy from 20 frame or I have to increase?).
I used this script to calculate binding energy and entropy on two complex. Is this script right for above calculation?
&general
endframe=10000, interval=10, keep_files=2, debug_printlevel=2,
/
&gb
igb=2, saltcon=0.100,
/
&nmode
nmstartframe=1, nmendframe=10000,
nminterval=50, nmode_igb=1, nmode_istrng=0.1,
/
I got this result from two caluclations: See an attachment!!
Why Nmode calculation is differ in frame numbers??
Thanks
Sonu
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Received on Wed May 09 2012 - 09:30:03 PDT
