On 26/03/2010 3:26 AM, Sikandar Mashayak wrote:
@ Mark :: you said if the potential is never used then I dont have to
worry about storing its value. Suppose I am replacing Coulombic
interactions with something of its equivalent through new force field,
and I dont store the potential due to it, will I still get the similar
results in terms of structure (RDF). Of course I am assuming that new
force can accurately replace the Coulombic interactions among the
charged atoms.
By just having correct forces acting on the atoms and not worrying about
storing potential energies, will I still get same trajectory as with
storing potential energies.
Yes, if the potential is never used. In principle, MD is integrating
Newton's Laws, which generally don't require the energy to be known.
Whether that is true depends on details of your simulation protocol that
we don't know. REMD, being a Monte Carlo method, needs an accurate
potential. Free-energy methods might need an accurate potential.
Generally speaking, equilibrium MD doesn't need it, however. You can
roughly test for this by adding some arbitrarily large value to the
energy (e.g. 10^90) and see if the subsequent MD breaks. First, do your
homework about how the algorithms you're using work... :-)
Mark
On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole <[email protected]
<mailto:[email protected]>> wrote:
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]
<mailto:[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]
<mailto:[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] <mailto:[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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