[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Bala S think_beyond at aol.com
Fri Apr 27 09:31:00 CEST 2012

Dear Justin

Thanks for the explanation.

I am following your tutorial of KALP membrane simulation. I am stuck in
between two steps of InflateGRO. After the first step, the tutorial requests
to perform EM. Should I be running grompp with new system_inflated.gro file
to generate a new .tpr file for EM or should I perform EM with em.tpr which
was generated some time back in the tutorial? The latter ran EM but the
former shows error 'number of coordinates in coordinate file
(system_inflated.gro, 6438)
             does not match topology (topol.top, 17403)"


Bala S

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