hbond restraint simulation

From: Prabir Khatua (
Date: Fri Jan 25 2019 - 13:19:24 CST

Dear NAMD user,

I am trying to prepare a barrel-shaped oligomer of a protein starting from
a monomer. I had
already such a barrel-shaped tetramer structure that I am using as
template. Now I am using this tetramer and a dimer from this tetramer
placed sufficiantly at optimal distance after avoiding the bad contacts to
prepare the hexamer. Only restriction that I need to form such a hexamer is
hydrogen bonds between a set of atoms. I am using 54 hbond restraints of
which 44 hbonds are already preformed and 10 hbonds are to be formed by the
simulation. I am wondering how to decide the force constant to speed up the
simulation to achieve the target structure. Please note that I do not need
a smooth free energy profile for this as I am interested to prepare the
hexamer only that will be used in the final simulation. Here, I am
attaching the colvar config file that I am using for the simulation. It
seems that the molecules are not moving at all which is likely due to the
bad choice of force constant. I am using the initial centers values for
this case is the distance between donor and acceptor atom. Can anyone
please suggest me an idea how to choose the force constant for my purpose
or what parameters to be tuned to speed up this process? Please also point
out if I am doing anything wrong in preparing the colvar config file.

Thanking you,


*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*

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