[gmx-users] Re: forces from trajectory

Mark Abraham mark.abraham at anu.edu.au
Fri Oct 8 19:03:14 CEST 2010

I'd take a look at do_md in src/kernel/md.c and see for myself :-)

I think the question is moot, because I have the off-hand impression that, for the md integrator, constraints are not implemented through modifying the force vectors, but rather imposed by the constraint algorithm upon the post-integration positions. I could be wrong - I've never needed to look at that code - but if the force vector is not being passed to the constraint routine...


----- Original Message -----
From: Sikandar Mashayak <symashayak at gmail.com>
Date: Saturday, October 9, 2010 3:29
Subject: [gmx-users] Re: forces from trajectory
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Could anyone please clarify on my previous question? I am very confused about the force value issue. 
> thanks
> sikandar
> On Thu, Oct 7, 2010 at 2:27 PM, Sikandar Mashayak <symashayak at gmail.com> wrote:
 > Hi
> In the post-processing ( analysis) code using gromacs trajectory, I access force values on atom using fr.x[indx_atm][XX]. The confusion I have is that " what force is it? is it the force before constraints ( fixed bonds) are applied or is it the effective force due to atom-atom interactions plus any constraints?"
> thanks
> sikandar
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