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

[Mark Abraham]

On 26/03/2010 7:07 AM, Sikandar Mashayak wrote:
> @ 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

Did it run without using tables?

Mark

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