[gmx-users] Fwd: calculation of forces during a trajectory

[David van der Spoel]

On Tue, 2005-03-08 at 14:35 +0200, Michael wrote:
> Dear Dr. Hess,
> 
> Thank you for your kind reply.
> 
> I just wanted to ask two more questions.
> 1) How do i set the LJ parameters to 0 ?
> 2) How do i set the bonded parameters of water molecules to 0?
> 
chapter 5 in the manual

> Thanks in Advance,
> Michael
> 
> On Mar 8, 2005, at 11:06 AM, Berk Hess wrote:
> 
> >
> >
> >
> >> From: Michael <mgang at pob.huji.ac.il>
> >> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Subject: [gmx-users] Fwd: calculation of forces during a trajectory
> >> Date: Tue, 8 Mar 2005 10:36:02 +0200
> >>
> >>
> >> Hi everybody,
> >>
> >> I wanted to list the coulombic forces on a particular atom during an
> >> MD
> >> run as a function of time.
> >> I searched in the manual and archive of the mailing group and did not
> >> find how to achieve this.
> >> I just found how to list the total force on a particular atom but not
> >> the coulombic force alone.
> >
> > You can not have access to the coulombic force alone.
> > The only way is to get is forces is mdrun -rerun on the trajectory
> > that you have produced with a normal mdrun.
> > For the rerun you will have to use a topology with all bonded and LJ
> > parameters set to 0.
> >
> > Berk.
> >
> > _________________________________________________________________
> > Talk with your online friends with MSN Messenger
> > http://messenger.msn.nl/
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++