[gmx-users] dummy atom - regd

ramesh cheerla rameshgromacs at gmail.com
Sun Feb 17 19:00:34 CET 2013

Dear gromacs users,

             I have defined a non-bonded atom, which has  no van der waals
as well as  electrostatic parameters ( i.e  the  atom should not  interact
with any other atoms in the system) and  more over its kinetic energy
should not contribute to the total energy of the system for this purpose I
have taken mass of  the system to be almost equal to zero. Now  I want to
freeze the position of this atom to measure the distance between the other
mobile atom with respect to this immobile reference.  To freeze the
position of atom I have used the following options in my  .mdp file:
freezegrps = PEGR
freezedim  = Y Y Y
 with the above mentioned options I was able to fix the position of  dummy
atom in NVT equilibration, but  in case of NPT equilibration at elevated
temperatures the position of dummy atom is  changing.  I have tried the
same thing with the position restraints also by using very high force
constant but I couldn't  succeeded.  am I making any mistake here ?  or is
there any better option to have a immobile
reference in my system to measure distance between mobile and immobile
one  along a particular axis ?

Any help will be highly  appreciated.


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