Dear all,
After following the aMD tutorial, I carried out a 500 ns long aMD
simulation using pmemd. The unfolded peptide was solvated in water and
chloroform box.
The calculation finished without any error reports and after analysis
everything seems fine. The phi-psi plots as function of free energy also
seem okay.
The problem is with re-weighting results. When I plot phi-psi as function
of PMF, the PMF (in kcal/mol) reaches the highest value of 400 in water
while remains around only 20 in chloroform.
Because of this, few conformations close to 0 kcal/mol exist on the free
energy surface. Till now, I could only find one more result with very high
PMF ~1200 kJ/mol which is comparable to mine. Is it normal to have such
high PMF values? What does it say about the simulation?
The below image is for one residue. Although, the secondary structure
conformations are expected. What role does the solvent play in aMD ?
Any suggestion is well appreciated.
--
Best wishes
Chetna Tyagi,
University of Szeged
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Received on Sun Jun 03 2018 - 07:30:03 PDT
