[gmx-users] dihedral restraint MD

Lin Huang 578944118 at qq.com
Tue Jun 12 18:12:23 CEST 2012

Hello Everyone,

I was willing to conduct umbrella sampling on the dihedrals derived from the
sidechains of a ion channel. So i tried dihedral restraint to achieve the
goal. However I encountered an awkward problem, hope someone can help me
with that.
The dihedrals of the initial conformation I used in my MD is -60 and 153
degree, respectively for phi and psi. And then I restricted both of them to
180 degree and conducted the dihedral restraint MD for 2ns. However the
dihedral analysis of my final result was quite awkward, since they kept on
fluctuating just around their initial value during this 2ns MD process. At
first, I considered maybe it was caused by the small restraint force
constant, which was set as 100 in my .mdp file. Nevertheless, after I
changed it to 500, no better result was given out. I am wondering whether
the energy barrier is too high for them to cross, so in the 2ns short MD
process, they have to move around their initial configuration. If this is
the key to my problem, how can I solve this problem?
Many thanks in advance. 

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