Dear Amber Users:
I've encountered some problems with the internal energy calculated by
MMPBSA.pl, I only have one chain in the system, and I removed water before
the calculation. But the result showed that the internal energy is
increasing linearly along with the temperature, I separated the bonded
energy, angle energy and dihedral energy but found out they were all
increasing linearly with the temperature.
The data I used was the average through out the total simulation time. I
can understand that with higher temperature, the internal energy might
be fluctuating in a larger range, but the average is also increasing
linearly? This increasing made the total energy of the chain a positive
number, but in fact the chain is collapsing. Which is very confusing to
me...Is it the way that amber calculates the energy? Force field?
Hope you guys could help me here, any suggestions would be really
appreciative. Thanks!!!
-Binwu
--
Binwu Zhao
Dept of Chemical and Biomolecular Engineerig
NCSU
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Received on Mon Aug 13 2012 - 08:30:03 PDT
