[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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