[gmx-users] polarizable ff and free energy calculation
Mark.Abraham at anu.edu.au
Wed Apr 18 18:18:38 CEST 2012
On 18/04/2012 10:32 PM, Tom Kirchner wrote:
> 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.
They came through.
> 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.
Thanks for the clear report.
> 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.
... well, likely some kind of floating-point-algebra failure, anyway.
> 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.
I've uploaded a draft fix to https://gerrit.gromacs.org/#/c/746/
> Moreover I'm wondering about the physical meaning of the if-statement.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users