[gmx-users] Switching off Coulombs for a charge group.

[David]

On Thu, 2004-11-18 at 14:37 -0500, Pradip Kumar Biswas wrote:
> Thank you very much David.  I have to set myself within your first  
> alternative. Your last alternative of setting the corresponding charges  
> to zero in the input will not help me as I want the Coul & vdw forces  
> be calculated for those charges but I only want to suppress energy for  
> the coulomb arising from those charges. I realize (?) that there are  
> three copies of the array chargeA[i] in t_mdatoms.
> for i=0; <md->nr; i++
> the first one extends from 0 to md->nr-1
> the 2nd one extends from md->nr to 2*md->nr-1
> the 3rd one extends from 2*md->nr to 3*md->nr-1
That doesn't look correct. Check src/mdlib/mdatom.c
> 
> Am I making a mistake here? I didn't find any segmentation fault when I  
> set the corresponding charges in all the three arrays to zero.
> 
> Can you please tell me the idea behind the three copies? That means are  
> they there for the calculation of energy from arrays-1&2 and  
> calculation of force from arrays-1&3; or something like that?  Thanking  
> you again in advance.
This has to do with free energy calculations where charges can change
from value qA to qB.

For normal simulations only A is used.
> 
> Best regards,
> Pradip.
> 
> On Nov 18, 2004, at 1:56 PM, David wrote:
> 
> > On Thu, 2004-11-18 at 13:37 -0500, Pradip Kumar Biswas wrote:
> >> Hi,
> >> Can anyone please tell me what's the best way in Gromacs to switch-off
> >> all the Coulomb interactions related to a particular charge group?
> >>
> >> I tried with setting the corresponding charges in the chargeA arrays  
> >> to
> >> zero
> >> by setting the following lines in a loop before going to "do_fnbf()":
> >>
> >> md->chargeA[i]  = 0 ;
> >> md->chargeA[i+md->nr]  = 0 ;
> >> md->chargeA[i+2*md->nr]  = 0 ;
> >>
> > you'd probably rather write
> > md->chargeA[i]  = 0 ;
> > md->chargeA[i+1]  = 0 ;
> > md->chargeA[i+2]  = 0 ;
> >
> > Since md->nr is the length of the array your code would generate a  
> > segmentation violation.
> >
> > Alternatively you could set the charges to zero in the input.
> >
> >> when [i] correspond to the desired charge.
> >>
> >> Can anyone suggest me how this setting inside Gromacs can jeopardize
> >> anything else that I cannot see at this moment?
> >> Thanking you in advance.
> >>
> >> Pradip.
> >> CSU, Ohio.
> >>
> >> _______________________________________________
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> > --  
> > David.
> > _______________________________________________________________________ 
> > _
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org    
> > http://xray.bmc.uu.se/~spoel
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> > +
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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