Aaron Fafarman wrote:
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
below:
....
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
iatoms:
0 type=364 (VSITE2) 1796 210 211
....
Thanks in advance for your help.
-Aaron
Message: 5
Date: Thu, 05 Jun 2008 08:53:32 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculating electric field vector at
snapshots
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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.
It could be that the force is set to zero after distributing it. Check
the src/mdlib/vsite.c code. You could modify this code, such that it
does not reset the forces. Be careful that this does not generate other
problems (you can check by comparing runs with and without this feature
using gmxcheck -e -e2 -tol 0).
The proper way to do this would be to recompute the non-bonded forces
(short range only) with LJ parameters set to zero. The contribution to
potential and field from PME can be extracted without too much trouble.
Thanks,
-Aaron
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
