[gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Erik Lindahl lindahl at cbr.su.se
Wed Aug 15 20:49:46 CEST 2007

Hi Jeroen,

Just set the charges to zero - then the program will automatically  
detect it and use LJ-only loops everywhere.



On Aug 15, 2007, at 8:12 PM, van Bemmelen wrote:

> Hi all,
> As a side note: although I also have some trouble figuring out what
> Nicolas Schmidt is exactly trying to do, I find the question "what  
> to do
> to totally switch the electrostatics off?" to be quite intriguing.  
> It is
> my understanding that when you simply set rcoulomb=0, this actually
> means an infinite cutoff. This is only of real use with pbc=no when
> simulating in vacuo.
> So can it be done in standard GROMACS? Can you set the mdp- 
> parameters in
> such a way, that GROMACS simply skips the electrostatics calculation
> altogether, thereby saving valuable computer time in systems without
> charges? Or will GROMACS simply detect that there are no charges
> whatsoever in the system, and automatically skip all the Coulomb
> calculations? Or will GROMACS always calculate the electrostatics,  
> even
> if there are no charges present, and simply fill in zeroes for all
> charges throughout the entire calculation?
> Just being curious. :-)
> Greetings,
> Jeroen
>>> Still: Though I thought I don't have to specify the
>>> electrostatics-section since my molecule doesn't have any
>> charges (or
>>> does it???), what to do to totally switch the electrostatics off?
>> You should be reading section 7.3 of the manual closely and
>> making these
>> choices actively, with reference to earlier in the manual
>> where needed.
>> You'll need to understand well how both this other software
>> and GROMACS
>> are doing the calculation in order to duplicate the ensemble  
>> averages.
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