[gmx-users] position restraint on some solvent molecules

Valentin Gogonea v.gogonea at csuohio.edu
Mon Jun 2 16:40:01 CEST 2003

Dear GROMACS users,

Is it possible to impose position restraints on only a selected subset 
of solvent molecules. If yes, how can this be indicated in the topology 
file? If this is not possible, can anybody point to me to the function 
in the GROMACS code which sets up the position restraints for solvent?

The second question concerns simulation with frozen groups. I was 
struggling for the past couple of weeks to perform a simulation in 
which part of a protein and solvent is frozen (using the spc model for 
water). It happens that after a while a moving water molecule collides 
with (getting very close to) a frozen water molecule and the simulation 
crashes giving NaN for coordinates of one water molecule and NaN for 
energy. I was thinking to impose position restraints for frozen water 
molecules which are accessible to moving water molecules, but I didn't 
figure out how this can be done.

Any help will be greatly appreciated.

Thank you,


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