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

[XAvier Periole]

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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