[gmx-users] Fwd: calculation of forces during a trajectory
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 8 13:43:58 CET 2005
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,
> 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.
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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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