Hi,
So I am trying to calculate the entropy of a system that I have simulated
for 100ns, and also to check it for convergence. It seems that the entropy
increases (becomes more negative) the more simulation-data is included in
the calculation, but it increases in a systematic way that does not make
sense to me...
I have calculated the entropy using MMPBSA.py with PTRAJ option.
I have calculated the entropy from the simulation in different chunks to
check the convergence....
# 10 ns chunks
0-10ns
10-20ns
20-30ns
...
90-100ns
# 20 ns chunks
0-20ns
10-30ns
...
80-100ns
#....
# 100ns chunks
0-100ns
For the 10ns chunks the results end at around -225 kcal/mole
For the 20ns chunks the results end at around -390 kcal/mole
For the 40ns chunks the results end at around -700 kcal/mole
For the 100ns chunk the results end at around -1400 kcal/mole
Can this be right? - should the number systematically increase with the
simulation length? It is only the vibrational part that varies
significantly.
The numbers surprise me a bit. As an example here are the results for the
0-100 ns chunk (using 500 frames):
Translational Rotational Vibrational Total
Complex: 17.0998 16.3344 1973.1877 2006.6222
Receptor: 17.0524 16.2936 1965.0449 1998.3912
Ligand: 14.4737 14.3574 1428.4709 1457.3017
DELTA S: -14.4263 -14.3166 -1420.3282 -1449.0707
The difference in vibrational entropy for the complex and receptor compared
to the ligand seems WAY too small, especially compared to values that I get
from a quick calculation using MMPBSA.PY with NAB for the entropy (although
here I have only used 50 frames - in the interest of time).
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.0998 0.0000
Rotational: 17.6933 0.0073
Vibrational: 3716.0164 6.8456
Total: 3750.8096 6.8495
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.0524 0.0000
Rotational: 17.6272 0.0129
Vibrational: 3528.2633 7.5486
Total: 3562.9430 7.5557
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 14.4737 0.0000
Rotational: 13.9148 0.1747
Vibrational: 213.2078 5.1222
Total: 241.5962 5.2772
DELTA S total= -53.7296 +/- 10.0718
I hope you can help me understand where the systematic error (if it is an
error) comes in...
Best,
Jesper
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Received on Mon May 16 2011 - 06:30:02 PDT
