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

[Sikandar Mashayak]

@ Xavier :: I am trying out table approach also. But I am facing some issues
with it. To start with , as a test run, i use GROMACS provided table6-12.xvg
table for LJ interactions. Using this table I am running water bulk
simulations. In mdp file I specify to use PME for electrostatics and User
for LJ by providing the table6-12.xvg file. But the simulation crashes with
the notes ::t = 0.000 ps: Water molecule starting at atom 5363 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

thanks
sikandar

On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak <symashayak at gmail.com>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.
>
> 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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