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

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 19 10:16:49 CET 2004


On Fri, 2004-11-19 at 10:22 +0800, Sandeep Somani wrote:
> 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.
> ...
> "
yes that would work
> 
> 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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-- 
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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