[gmx-users] CG Force and Potential through do_force()
Sikandar Mashayak
symashayak at gmail.com
Thu Mar 25 21:56:31 CET 2010
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.
thanks
sikandar
On Thu, Mar 25, 2010 at 3:43 PM, Mark Abraham <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>> 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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>>
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