On Wed, May 9, 2012 at 12:09 PM, Kumar, Sonu
<sonu.kumar.dkfz-heidelberg.de>wrote:
> 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??
>
nmstartframe, nmendframe, and nminterval correspond to subsets taken from
what you get from startframe, endframe, and interval in &general. For
instance, you will be extracting 1000 frames for the GB calculation. You
now select one from every 50 of these snapshots (or 20 total snapshots).
If you want 200 snapshots, set nminterval=5 instead.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 09 2012 - 12:30:03 PDT
