[gmx-users] polarizable ff and free energy calculation

Tom Kirchner tomkirch at mis.mpg.de
Wed Apr 18 14:32:22 CEST 2012

Of my first mail, only the attachment was printed in the mailing list. I 
am sorry for the inconvenience. The attachment can be sent by request.


Hi all,

Recently, I posted a problem concerning the usage of polarizable ff in 
conjunction with free energy calculation. Sadly I got no answer, but 
after some research, I hope I have isolated the problem.

Using a polarizable ff without free energy makes no problems. As soon as 
free energy is turned on, Gromacs gives the error:

/Program mdrun_d, VERSION 4.5.5
Source code file: [...]/src/gromacs-4.5.5/src/mdlib/shellfc.c, line: 365

Fatal error:
polarize can not be used with qA != qB/

This error occurs, even if the atom and the shell particle have the same 
charge or are unaltered by the free energy option, e.g. lambda=0.0 and 
multiplication with (1-lambda). Because of this, I guess there is a 
problem with different charge variables being single and double 
precision due to multiplication with lambda.

The error occurs in this segment of shellfc.c:

         case F_POLARIZATION:
           if (qS != atom[aS].qB)
         gmx_fatal(FARGS,"polarize can not be used with qA != qB");

If anybody knows, how to correct this, I would be very grateful.
Moreover I'm wondering about the physical meaning of the if-statement.

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