[AMBER] Negative dihedral angle n glycan simulation

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Tue, 2 Apr 2019 16:34:58 +0530

Dear AMBER user and developers,
I am trying to simulate a proteoglycan structure using conventional
molecular dynamics technique. Everything seems to be fine in the output
file where only the dihedral energy is showing a negative value. So why am
I getting the negative value in dihedral energy? Is there any discrepancy
in my system?
Secondly, when I am trying to simulate the same system using amd or gamd in
dual boost mode, but dihedral boost potential remains zero throughout our
simulation. As discussed in the gamd archive it is because of the negative
dihedral energy.
So is it an error to get negative dihedral energy or can I use the single
potential boost in amd or gamd technique?
It will be beneficial for me if you clarify all these doubts.
Thank you in advance!

*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
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Received on Tue Apr 02 2019 - 04:30:02 PDT
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