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

[Sandeep Somani]

hi 

am curious .. cant we just use tpbconv to switch off couloub charges ? 
the help says: 
"
...
 3rd. by setting the charges of a specified group to zero. This is
useful when doing free energy estimates using the LIE (Linear Interactio
Energy) method.
...
"

rgds
sandeep





> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David
> Sent: Friday, November 19, 2004 4:02 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Switching off Coulombs for a charge group.
> 
> 
> 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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> 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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