[gmx-users] CG Force and Potential through do_force()
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Mar 25 22:09:04 CET 2010
On 26/03/2010 7:56 AM, Sikandar Mashayak wrote:
> Thanks Mark for the explanation. Yeah, definitely I need to go through
> the algorithms that GROMACS use.
> As far Table approach is concerned, same simulation set up worked
> without using Table.
Well, you've probably done it wrong, but we don't have enough
information to say where...
Mark
> On Thu, Mar 25, 2010 at 3:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> 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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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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