[gmx-users] Position restraints and double precision

[Miguel Caro]

Hi all,

I am trying to do an MD simulation of a small hexagonal box where I need 
some of the atoms to stay fixed. This is because I am mixing ab initio 
and classical MD and some of the atoms in my system should remain within 
the configuration predicted by DFT.

As far as I know, GROMACS only allows energy penalties, rather than true 
position constraints, and so I have to resort to extremely high energy 
penalties for some of the atoms:

    [ position_restraints ]
    ;  i funct       fcx        fcy        fcz
        1    1       100000000       100000000       100000000
        2    1       100000000       100000000       100000000
    etc...

The above restraints still lead to a small oscillation of the "fixed" 
atoms. These numbers being so large means that the number of significant 
figures allowed for the total energy during the energy minimization is 
limited to very few decimal places using single precision. As a matter 
of fact, GROMACS complains that convergence to machine precision is 
achieved before the required precision.

I guess I have two questions:

1) Why do I need such huge energy penalties to fix my atoms?

2) Will the precision issue also affect an MD run or only the EM run? 
Should I reinstall GROMACS in double precision?

Miguel
-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba at gmail.com*
Work: *miguel.caro at aalto.fi*
Website: http://mcaroba.dyndns.org