[gmx-users] Calculating electric field vector at snapshots

Aaron Fafarman aarontf at stanford.edu
Mon Jul 14 19:25:21 CEST 2008

Thank you for considering my proposed scheme for calculating the
electric field vector at a single site at every snapshot of an MD
trajectory. As discussed previously on this list, I have attempted to
use a virtual site with no mass and with an infinitesimal charge,
constructed from two atoms in the region of interest, and printing the
output of the force on the virtual site at every step.  The problem I
have run into is that the force on the virtual site is zero at every
step (see gmxdump below ) . I think this is because mdrun has already
redistributed the forces from the virtual site to the constructing
particles. Is there a way (a small code modification perhaps) that I
could capture the information of the force on the virtual sites before
it's been redistributed?

excerpt from gmxdump of trajectory from mdrun with integrator = md;
atom 1796 is the virtual site
      f[ 1795]={ 8.67412e+02, -1.41267e+02,  2.31425e+02}
      f[ 1796]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      f[ 1797]={-3.19446e+02, -1.38371e+03, -8.82301e+02}

Just in case there's some other explanation for the zero forces, I've
also included excerpts of the output of the gmxdump of the .tpr file
atom[  1796]={type=  9, typeB=  9, ptype=   VSite, m= 0.00000e+00, q=
1.00000e-04, mB= 0.00000e+00, qB= 1.00000e-04, resnr=  119} grpnrs=[ 0
0 0 0 0 0 0 0 0 0 ]}
Virtual site 2:
            nr: 4
            multinr[division over processors]: 4
               0 type=364 (VSITE2) 1796 210 211

Thanks in advance for your help.


> Message: 5
> Date: Thu, 05 Jun 2008 08:53:32 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Calculating electric field vector at
>        snapshots
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48478D6C.3050904 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Aaron Fafarman wrote:
>> Dear GMX community,
>> I would like to calculate the electric field vector at a point in
>> space in a protein at many snapshots during an MD trajectory. I
>> haven't found a built-in function for doing this in Gromacs--is there
>> one? If not, would people please comment on this proposal for how to
>> do this:
>> 1. Include a virtual site referenced to the two atoms (constructing
>> particles) that define the point in space I would like to interrogate.
>> Give it only a very small charge, so small that the force from the
>> virtual site to the constructing particles is negligible.
>> 2. Have the calculation output the force on the virtual site at a
>> determined interval by setting nstfout in the.mdp file
>> 3. Divide the force by the small charge, and hence get the field
>> It seems like this should work as long as the force on virtual sites
>> is reported in the output of forces from nstfout, and as long as using
>> such a small charge on the virtual site will not run into rounding
>> errors. Also I'm presuming that the coulomb interaction is not
>> calculated between the constructing atoms and the virtual site--is
>> that correct? Any thoughts?
> I think it will work. Just try it.
>> Thanks,
>> -Aaron
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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
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