[gmx-users] CG Force and Potential through do_force()

[Sikandar Mashayak]

@ 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.

thanks
sikandar

On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole <x.periole at rug.nl> 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 <symashayak at gmail.com>
>> Date: Thursday, March 25, 2010 15:12
>> Subject: Re: [gmx-users] CG Force and Potential through do_force()
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>>  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 <Mark.Abraham at anu.edu.au>
>>> 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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