If your force is between "atom" pairs you might be better trying to
give all
of that as a tabulated potential ... no coding.
On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote:
----- Original Message -----
From: Sikandar Mashayak <[email protected]>
Date: Thursday, March 25, 2010 15:12
Subject: Re: [gmx-users] CG Force and Potential through do_force()
To: Discussion list for GROMACS users <[email protected]>
well if I need to add it by myself, I am not very sure in what
variable to add it to. Like I said, I know to add the force on the
atom i do f[indxofatom][XX]= forcevalue, where to potential value
due to this force?
It's not easy. Look at how the generic kernel does it and work you
way back through the data structures.
Mark
On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham <[email protected]
> wrote:
On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:
Hi
I want to do Coarse-Grained simulation in Gromacs. I have one CG force
formula, which I plan to implement by adding a short code in
do_force()
routine in Gromacs 4.0.7 source code.
After browsing through the do_force() code, I am now familiar with
data
structure relevant to add the new force. I mean, I can specify new
force
by adding to f[indx][XX] and so on.
But I am not very sure about potential, whether do I have to
explicitly
specify the potential on atoms due to this force or gromacs
automatically takes care of it by knowing the forces on each atoms?
You will need to add that yourself if you want the reported
potential to be accurate. GROMACS uses the given parameters in its
inner loops to calculate energies and forces. The former are not
reverse-engineered from the latter. If the potential is never used,
however, then you can forget about it...
Mark
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