@ 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 <[email protected]>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 <[email protected]> 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 <[email protected]> >>> Date: Thursday, March 25, 2010 15:12 >>> Subject: Re: [gmx-users] CG Force and Potential through do_force() >>> To: Discussion list for GROMACS users <[email protected]> >>> >>> 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 <[email protected]> >>>> 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 >>> >>>> >>>> -- >>> >>>> >>>> gmx-users mailing list [email protected] >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> >>>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> >>>> >>>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected]. >>> >>>> >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>>> >>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search >>>> before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected]. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to [email protected]. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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